vst transformation is feasible, but failed executing the next command #15
Comments
|
Hi Moh,
Thank you for your question. This seems to be caused by the sparsity of
your simulated data. If you run vst (from the DEseq2 package) on your
dataset, it gives the same error, which means that there are less than
'nsub'(nsub=1000) rows with mean normalized count > 5.
I added an argument of if.vst in the run.Ted function, to allow you to
bypass the vst step. Simply set if.vst=FALSE, to disable vst.
Let me know if there are any questions.
Best,
Tinyi
…On Sat, Jan 15, 2022 at 7:30 PM Moh Huda ***@***.***> wrote:
I have some different types of data (real data, semisynthetic data, and
fully synthetic data generated using splatter software). When running the
data and got the message "every gene has at least one zero. vst
transformation is NOT feasible”, the running process is successful.
However, when running different data and got the message "vst
transformation is feasible" the execution failed (running process failed).
The error message is
1. "Error in vst(Zkg.tum.round, nsub = min(nrow(Zkg.tum.round)/5,
1000)) :
less than 'nsub' rows with mean normalized count > 5,
it is recommended to use varianceStabilizingTransformation directly".
I check the file called runTed.R and this command is in line 335. The
suggestion there said that,
1. #adjust nsub, to avoid error when too few genes are used
What I understand that I need to change the function vst() on the line
335 to varianceStabilizingTransformation(), but it does not work either.
Also, I have no idea how to adjust nsub (the suggestion number 2 above).
Could you please give a suggestion? Thank you.
I attach the two sample data types.
rstudio-export-2.zip
<https://github.com/Danko-Lab/TED/files/7876152/rstudio-export-2.zip>
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Dear Tinyi,
I want to confirm that the line I need to modify is line 335 from
if(if.vst){
becoming if(if.vst=FALSE){
Is that all? Thank you very much for your help and reply.
Best regards,
Huda
…On Mon, 17 Jan 2022, 07:40 Tinyi Chu, ***@***.***> wrote:
Hi Moh,
Thank you for your question. This seems to be caused by the sparsity of
your simulated data. If you run vst (from the DEseq2 package) on your
dataset, it gives the same error, which means that there are less than
'nsub'(nsub=1000) rows with mean normalized count > 5.
I added an argument of if.vst in the run.Ted function, to allow you to
bypass the vst step. Simply set if.vst=FALSE, to disable vst.
Let me know if there are any questions.
Best,
Tinyi
On Sat, Jan 15, 2022 at 7:30 PM Moh Huda ***@***.***> wrote:
> I have some different types of data (real data, semisynthetic data, and
> fully synthetic data generated using splatter software). When running the
> data and got the message "every gene has at least one zero. vst
> transformation is NOT feasible”, the running process is successful.
> However, when running different data and got the message "vst
> transformation is feasible" the execution failed (running process
failed).
> The error message is
>
> 1. "Error in vst(Zkg.tum.round, nsub = min(nrow(Zkg.tum.round)/5,
> 1000)) :
> less than 'nsub' rows with mean normalized count > 5,
> it is recommended to use varianceStabilizingTransformation directly".
>
> I check the file called runTed.R and this command is in line 335. The
> suggestion there said that,
>
> 1. #adjust nsub, to avoid error when too few genes are used
> What I understand that I need to change the function vst() on the line
> 335 to varianceStabilizingTransformation(), but it does not work either.
> Also, I have no idea how to adjust nsub (the suggestion number 2 above).
>
> Could you please give a suggestion? Thank you.
>
> I attach the two sample data types.
> rstudio-export-2.zip
> <https://github.com/Danko-Lab/TED/files/7876152/rstudio-export-2.zip>
>
> —
> Reply to this email directly, view it on GitHub
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Hi Huda,
No, you do not need to change the code. You only need to re-install the
updated package, and put if.vst=FALSE in the function argument.
Best,
Tinyi
…On Mon, Jan 17, 2022 at 8:00 AM Moh Huda ***@***.***> wrote:
Dear Tinyi,
I want to confirm that the line I need to modify is line 335 from
if(if.vst){
becoming if(if.vst=FALSE){
Is that all? Thank you very much for your help and reply.
Best regards,
Huda
On Mon, 17 Jan 2022, 07:40 Tinyi Chu, ***@***.***> wrote:
> Hi Moh,
>
> Thank you for your question. This seems to be caused by the sparsity of
> your simulated data. If you run vst (from the DEseq2 package) on your
> dataset, it gives the same error, which means that there are less than
> 'nsub'(nsub=1000) rows with mean normalized count > 5.
>
> I added an argument of if.vst in the run.Ted function, to allow you to
> bypass the vst step. Simply set if.vst=FALSE, to disable vst.
>
> Let me know if there are any questions.
>
> Best,
>
> Tinyi
>
>
> On Sat, Jan 15, 2022 at 7:30 PM Moh Huda ***@***.***> wrote:
>
> > I have some different types of data (real data, semisynthetic data, and
> > fully synthetic data generated using splatter software). When running
the
> > data and got the message "every gene has at least one zero. vst
> > transformation is NOT feasible”, the running process is successful.
> > However, when running different data and got the message "vst
> > transformation is feasible" the execution failed (running process
> failed).
> > The error message is
> >
> > 1. "Error in vst(Zkg.tum.round, nsub = min(nrow(Zkg.tum.round)/5,
> > 1000)) :
> > less than 'nsub' rows with mean normalized count > 5,
> > it is recommended to use varianceStabilizingTransformation directly".
> >
> > I check the file called runTed.R and this command is in line 335. The
> > suggestion there said that,
> >
> > 1. #adjust nsub, to avoid error when too few genes are used
> > What I understand that I need to change the function vst() on the line
> > 335 to varianceStabilizingTransformation(), but it does not work
either.
> > Also, I have no idea how to adjust nsub (the suggestion number 2
above).
> >
> > Could you please give a suggestion? Thank you.
> >
> > I attach the two sample data types.
> > rstudio-export-2.zip
> > <https://github.com/Danko-Lab/TED/files/7876152/rstudio-export-2.zip>
> >
> > —
> > Reply to this email directly, view it on GitHub
> > <#15>, or unsubscribe
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Dear Tinyi,
I am currently using the RStudio server and the last time I installed
BayesPrism it was quite difficult and I need the admin help to resolve the
issue.
Could you please direct me to the updated version if possible?
When you said "put if.vst=FALSE in the function argument", you mean the
function run.Ted(..., if.vst=FALSE)?
I am sorry I am really bad at programming. Thank you for your help and
patience.
Regards,
Huda
…On Mon, 17 Jan 2022, 18:21 Tinyi Chu, ***@***.***> wrote:
Hi Huda,
No, you do not need to change the code. You only need to re-install the
updated package, and put if.vst=FALSE in the function argument.
Best,
Tinyi
On Mon, Jan 17, 2022 at 8:00 AM Moh Huda ***@***.***> wrote:
> Dear Tinyi,
>
>
> I want to confirm that the line I need to modify is line 335 from
> if(if.vst){
> becoming if(if.vst=FALSE){
>
> Is that all? Thank you very much for your help and reply.
>
>
> Best regards,
>
> Huda
>
> On Mon, 17 Jan 2022, 07:40 Tinyi Chu, ***@***.***> wrote:
>
> > Hi Moh,
> >
> > Thank you for your question. This seems to be caused by the sparsity of
> > your simulated data. If you run vst (from the DEseq2 package) on your
> > dataset, it gives the same error, which means that there are less than
> > 'nsub'(nsub=1000) rows with mean normalized count > 5.
> >
> > I added an argument of if.vst in the run.Ted function, to allow you to
> > bypass the vst step. Simply set if.vst=FALSE, to disable vst.
> >
> > Let me know if there are any questions.
> >
> > Best,
> >
> > Tinyi
> >
> >
> > On Sat, Jan 15, 2022 at 7:30 PM Moh Huda ***@***.***> wrote:
> >
> > > I have some different types of data (real data, semisynthetic data,
and
> > > fully synthetic data generated using splatter software). When running
> the
> > > data and got the message "every gene has at least one zero. vst
> > > transformation is NOT feasible”, the running process is successful.
> > > However, when running different data and got the message "vst
> > > transformation is feasible" the execution failed (running process
> > failed).
> > > The error message is
> > >
> > > 1. "Error in vst(Zkg.tum.round, nsub = min(nrow(Zkg.tum.round)/5,
> > > 1000)) :
> > > less than 'nsub' rows with mean normalized count > 5,
> > > it is recommended to use varianceStabilizingTransformation directly".
> > >
> > > I check the file called runTed.R and this command is in line 335. The
> > > suggestion there said that,
> > >
> > > 1. #adjust nsub, to avoid error when too few genes are used
> > > What I understand that I need to change the function vst() on the
line
> > > 335 to varianceStabilizingTransformation(), but it does not work
> either.
> > > Also, I have no idea how to adjust nsub (the suggestion number 2
> above).
> > >
> > > Could you please give a suggestion? Thank you.
> > >
> > > I attach the two sample data types.
> > > rstudio-export-2.zip
> > > <https://github.com/Danko-Lab/TED/files/7876152/rstudio-export-2.zip
>
> > >
> > > —
> > > Reply to this email directly, view it on GitHub
> > > <#15>, or unsubscribe
> > > <
> >
>
https://github.com/notifications/unsubscribe-auth/AB4NHS26BBA42WZU3PR72NDUWIGTVANCNFSM5MBTIUWA
> > >
> > > .
> > > Triage notifications on the go with GitHub Mobile for iOS
> > > <
> >
>
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> > > <
> >
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> > >.
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> > > You are receiving this because you are subscribed to this
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> > > ID: ***@***.***>
> > >
> >
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> > <#15 (comment)>,
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*Could you please direct me to the updated version if possible?*
The github repository was updated yesterday. You may simply follow the
instructions on https://github.com/Danko-Lab/TED to install (upgrade).
*When you said "put if.vst=FALSE in the function argument", you mean
thefunction run.Ted(..., if.vst=FALSE)?*
yes
…On Mon, Jan 17, 2022 at 1:31 PM Moh Huda ***@***.***> wrote:
Dear Tinyi,
I am currently using the RStudio server and the last time I installed
BayesPrism it was quite difficult and I need the admin help to resolve the
issue.
Could you please direct me to the updated version if possible?
When you said "put if.vst=FALSE in the function argument", you mean the
function run.Ted(..., if.vst=FALSE)?
I am sorry I am really bad at programming. Thank you for your help and
patience.
Regards,
Huda
On Mon, 17 Jan 2022, 18:21 Tinyi Chu, ***@***.***> wrote:
> Hi Huda,
>
> No, you do not need to change the code. You only need to re-install the
> updated package, and put if.vst=FALSE in the function argument.
>
> Best,
>
> Tinyi
>
> On Mon, Jan 17, 2022 at 8:00 AM Moh Huda ***@***.***> wrote:
>
> > Dear Tinyi,
> >
> >
> > I want to confirm that the line I need to modify is line 335 from
> > if(if.vst){
> > becoming if(if.vst=FALSE){
> >
> > Is that all? Thank you very much for your help and reply.
> >
> >
> > Best regards,
> >
> > Huda
> >
> > On Mon, 17 Jan 2022, 07:40 Tinyi Chu, ***@***.***> wrote:
> >
> > > Hi Moh,
> > >
> > > Thank you for your question. This seems to be caused by the sparsity
of
> > > your simulated data. If you run vst (from the DEseq2 package) on your
> > > dataset, it gives the same error, which means that there are less
than
> > > 'nsub'(nsub=1000) rows with mean normalized count > 5.
> > >
> > > I added an argument of if.vst in the run.Ted function, to allow you
to
> > > bypass the vst step. Simply set if.vst=FALSE, to disable vst.
> > >
> > > Let me know if there are any questions.
> > >
> > > Best,
> > >
> > > Tinyi
> > >
> > >
> > > On Sat, Jan 15, 2022 at 7:30 PM Moh Huda ***@***.***> wrote:
> > >
> > > > I have some different types of data (real data, semisynthetic data,
> and
> > > > fully synthetic data generated using splatter software). When
running
> > the
> > > > data and got the message "every gene has at least one zero. vst
> > > > transformation is NOT feasible”, the running process is successful.
> > > > However, when running different data and got the message "vst
> > > > transformation is feasible" the execution failed (running process
> > > failed).
> > > > The error message is
> > > >
> > > > 1. "Error in vst(Zkg.tum.round, nsub = min(nrow(Zkg.tum.round)/5,
> > > > 1000)) :
> > > > less than 'nsub' rows with mean normalized count > 5,
> > > > it is recommended to use varianceStabilizingTransformation
directly".
> > > >
> > > > I check the file called runTed.R and this command is in line 335.
The
> > > > suggestion there said that,
> > > >
> > > > 1. #adjust nsub, to avoid error when too few genes are used
> > > > What I understand that I need to change the function vst() on the
> line
> > > > 335 to varianceStabilizingTransformation(), but it does not work
> > either.
> > > > Also, I have no idea how to adjust nsub (the suggestion number 2
> > above).
> > > >
> > > > Could you please give a suggestion? Thank you.
> > > >
> > > > I attach the two sample data types.
> > > > rstudio-export-2.zip
> > > > <
https://github.com/Danko-Lab/TED/files/7876152/rstudio-export-2.zip
> >
> > > >
> > > > —
> > > > Reply to this email directly, view it on GitHub
> > > > <#15>, or unsubscribe
> > > > <
> > >
> >
>
https://github.com/notifications/unsubscribe-auth/AB4NHS26BBA42WZU3PR72NDUWIGTVANCNFSM5MBTIUWA
> > > >
> > > > .
> > > > Triage notifications on the go with GitHub Mobile for iOS
> > > > <
> > >
> >
>
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> > > >
> > > > or Android
> > > > <
> > >
> >
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>,
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Dear Tinyi,
Got it. Thank you very much.
Best regards,
Huda
Get Outlook for Android<https://aka.ms/AAb9ysg>
________________________________
From: Tinyi Chu ***@***.***>
Sent: Monday, January 17, 2022 6:36:48 PM
To: Danko-Lab/TED ***@***.***>
Cc: Moh Huda ***@***.***>; Author ***@***.***>
Subject: Re: [Danko-Lab/TED] vst transformation is feasible, but failed executing the next command (Issue #15)
*Could you please direct me to the updated version if possible?*
The github repository was updated yesterday. You may simply follow the
instructions on https://github.com/Danko-Lab/TED to install (upgrade).
*When you said "put if.vst=FALSE in the function argument", you mean
thefunction run.Ted(..., if.vst=FALSE)?*
yes
On Mon, Jan 17, 2022 at 1:31 PM Moh Huda ***@***.***> wrote:
Dear Tinyi,
I am currently using the RStudio server and the last time I installed
BayesPrism it was quite difficult and I need the admin help to resolve the
issue.
Could you please direct me to the updated version if possible?
When you said "put if.vst=FALSE in the function argument", you mean the
function run.Ted(..., if.vst=FALSE)?
I am sorry I am really bad at programming. Thank you for your help and
patience.
Regards,
Huda
On Mon, 17 Jan 2022, 18:21 Tinyi Chu, ***@***.***> wrote:
> Hi Huda,
>
> No, you do not need to change the code. You only need to re-install the
> updated package, and put if.vst=FALSE in the function argument.
>
> Best,
>
> Tinyi
>
> On Mon, Jan 17, 2022 at 8:00 AM Moh Huda ***@***.***> wrote:
>
> > Dear Tinyi,
> >
> >
> > I want to confirm that the line I need to modify is line 335 from
> > if(if.vst){
> > becoming if(if.vst=FALSE){
> >
> > Is that all? Thank you very much for your help and reply.
> >
> >
> > Best regards,
> >
> > Huda
> >
> > On Mon, 17 Jan 2022, 07:40 Tinyi Chu, ***@***.***> wrote:
> >
> > > Hi Moh,
> > >
> > > Thank you for your question. This seems to be caused by the sparsity
of
> > > your simulated data. If you run vst (from the DEseq2 package) on your
> > > dataset, it gives the same error, which means that there are less
than
> > > 'nsub'(nsub=1000) rows with mean normalized count > 5.
> > >
> > > I added an argument of if.vst in the run.Ted function, to allow you
to
> > > bypass the vst step. Simply set if.vst=FALSE, to disable vst.
> > >
> > > Let me know if there are any questions.
> > >
> > > Best,
> > >
> > > Tinyi
> > >
> > >
> > > On Sat, Jan 15, 2022 at 7:30 PM Moh Huda ***@***.***> wrote:
> > >
> > > > I have some different types of data (real data, semisynthetic data,
> and
> > > > fully synthetic data generated using splatter software). When
running
> > the
> > > > data and got the message "every gene has at least one zero. vst
> > > > transformation is NOT feasible”, the running process is successful.
> > > > However, when running different data and got the message "vst
> > > > transformation is feasible" the execution failed (running process
> > > failed).
> > > > The error message is
> > > >
> > > > 1. "Error in vst(Zkg.tum.round, nsub = min(nrow(Zkg.tum.round)/5,
> > > > 1000)) :
> > > > less than 'nsub' rows with mean normalized count > 5,
> > > > it is recommended to use varianceStabilizingTransformation
directly".
> > > >
> > > > I check the file called runTed.R and this command is in line 335.
The
> > > > suggestion there said that,
> > > >
> > > > 1. #adjust nsub, to avoid error when too few genes are used
> > > > What I understand that I need to change the function vst() on the
> line
> > > > 335 to varianceStabilizingTransformation(), but it does not work
> > either.
> > > > Also, I have no idea how to adjust nsub (the suggestion number 2
> > above).
> > > >
> > > > Could you please give a suggestion? Thank you.
> > > >
> > > > I attach the two sample data types.
> > > > rstudio-export-2.zip
> > > > <
https://github.com/Danko-Lab/TED/files/7876152/rstudio-export-2.zip
> >
> > > >
> > > > —
> > > > Reply to this email directly, view it on GitHub
> > > > <#15>, or unsubscribe
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Dear Tinyi,
I have updated the package TED in R and have added the argument if.vst = FALSE in runTED.R function This is to be precise what I have used run.Ted(ref.dat = filter_gene_scRNA_data, X = chosen_data, cell.type.labels = ***@***.***$seurat_clusters, cell.subtype.labels = ***@***.***$seurat_clusters, tum.key = "1", input.type = "scRNA", n.cores = 20, pdf.name = "tcga.tumor.synthetic", if.vst=FALSE). However, I got this error Error in run.Ted(ref.dat = filter_gene_scRNA_data, X = chosen_data, cell.type.labels = ***@***.***$seurat_clusters, :
unused argument (if.vst = FALSE).
1. I suppose I use the argument incorrectly. a) Then where should this argument be added then? b) Or is it possible that I might fail in updating the package which leads to this error message?
2. The version of the package TED I got is packageVersion("TED”) [1] ‘1.1’. Is it the correct one for the most updated?
Thank you very much.
Regards,
Huda
… On 17 Jan 2022, at 18:36, Tinyi Chu ***@***.***> wrote:
*Could you please direct me to the updated version if possible?*
The github repository was updated yesterday. You may simply follow the
instructions on https://github.com/Danko-Lab/TED to install (upgrade).
*When you said "put if.vst=FALSE in the function argument", you mean
thefunction run.Ted(..., if.vst=FALSE)?*
yes
On Mon, Jan 17, 2022 at 1:31 PM Moh Huda ***@***.***> wrote:
> Dear Tinyi,
>
> I am currently using the RStudio server and the last time I installed
> BayesPrism it was quite difficult and I need the admin help to resolve the
> issue.
>
> Could you please direct me to the updated version if possible?
>
> When you said "put if.vst=FALSE in the function argument", you mean the
> function run.Ted(..., if.vst=FALSE)?
>
> I am sorry I am really bad at programming. Thank you for your help and
> patience.
>
> Regards,
>
> Huda
>
> On Mon, 17 Jan 2022, 18:21 Tinyi Chu, ***@***.***> wrote:
>
> > Hi Huda,
> >
> > No, you do not need to change the code. You only need to re-install the
> > updated package, and put if.vst=FALSE in the function argument.
> >
> > Best,
> >
> > Tinyi
> >
> > On Mon, Jan 17, 2022 at 8:00 AM Moh Huda ***@***.***> wrote:
> >
> > > Dear Tinyi,
> > >
> > >
> > > I want to confirm that the line I need to modify is line 335 from
> > > if(if.vst){
> > > becoming if(if.vst=FALSE){
> > >
> > > Is that all? Thank you very much for your help and reply.
> > >
> > >
> > > Best regards,
> > >
> > > Huda
> > >
> > > On Mon, 17 Jan 2022, 07:40 Tinyi Chu, ***@***.***> wrote:
> > >
> > > > Hi Moh,
> > > >
> > > > Thank you for your question. This seems to be caused by the sparsity
> of
> > > > your simulated data. If you run vst (from the DEseq2 package) on your
> > > > dataset, it gives the same error, which means that there are less
> than
> > > > 'nsub'(nsub=1000) rows with mean normalized count > 5.
> > > >
> > > > I added an argument of if.vst in the run.Ted function, to allow you
> to
> > > > bypass the vst step. Simply set if.vst=FALSE, to disable vst.
> > > >
> > > > Let me know if there are any questions.
> > > >
> > > > Best,
> > > >
> > > > Tinyi
> > > >
> > > >
> > > > On Sat, Jan 15, 2022 at 7:30 PM Moh Huda ***@***.***> wrote:
> > > >
> > > > > I have some different types of data (real data, semisynthetic data,
> > and
> > > > > fully synthetic data generated using splatter software). When
> running
> > > the
> > > > > data and got the message "every gene has at least one zero. vst
> > > > > transformation is NOT feasible”, the running process is successful.
> > > > > However, when running different data and got the message "vst
> > > > > transformation is feasible" the execution failed (running process
> > > > failed).
> > > > > The error message is
> > > > >
> > > > > 1. "Error in vst(Zkg.tum.round, nsub = min(nrow(Zkg.tum.round)/5,
> > > > > 1000)) :
> > > > > less than 'nsub' rows with mean normalized count > 5,
> > > > > it is recommended to use varianceStabilizingTransformation
> directly".
> > > > >
> > > > > I check the file called runTed.R and this command is in line 335.
> The
> > > > > suggestion there said that,
> > > > >
> > > > > 1. #adjust nsub, to avoid error when too few genes are used
> > > > > What I understand that I need to change the function vst() on the
> > line
> > > > > 335 to varianceStabilizingTransformation(), but it does not work
> > > either.
> > > > > Also, I have no idea how to adjust nsub (the suggestion number 2
> > > above).
> > > > >
> > > > > Could you please give a suggestion? Thank you.
> > > > >
> > > > > I attach the two sample data types.
> > > > > rstudio-export-2.zip
> > > > > <
> https://github.com/Danko-Lab/TED/files/7876152/rstudio-export-2.zip
> > >
> > > > >
> > > > > —
> > > > > Reply to this email directly, view it on GitHub
> > > > > <#15>, or unsubscribe
> > > > > <
> > > >
> > >
> >
> https://github.com/notifications/unsubscribe-auth/AB4NHS26BBA42WZU3PR72NDUWIGTVANCNFSM5MBTIUWA
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> > > >
> > >
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> > >
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Hi Huda,
Yes. I think you did not update the package correctly. To check, you can
simply type run.Ted in your R console, and see if the argument if.vst is in
it.
Best,
Tinyi
…On Wed, Jan 19, 2022 at 3:54 PM Moh Huda ***@***.***> wrote:
Dear Tinyi,
I have updated the package TED in R and have added the argument if.vst =
FALSE in runTED.R function This is to be precise what I have used
run.Ted(ref.dat = filter_gene_scRNA_data, X = chosen_data, cell.type.labels
= ***@***.***$seurat_clusters, cell.subtype.labels =
***@***.***$seurat_clusters, tum.key = "1", input.type = "scRNA", n.cores =
20, pdf.name = "tcga.tumor.synthetic", if.vst=FALSE). However, I got this
error Error in run.Ted(ref.dat = filter_gene_scRNA_data, X = chosen_data,
cell.type.labels = ***@***.***$seurat_clusters, :
unused argument (if.vst = FALSE).
1. I suppose I use the argument incorrectly. a) Then where should this
argument be added then? b) Or is it possible that I might fail in updating
the package which leads to this error message?
2. The version of the package TED I got is packageVersion("TED”) [1]
‘1.1’. Is it the correct one for the most updated?
Thank you very much.
Regards,
Huda
> On 17 Jan 2022, at 18:36, Tinyi Chu ***@***.***> wrote:
>
>
> *Could you please direct me to the updated version if possible?*
> The github repository was updated yesterday. You may simply follow the
> instructions on https://github.com/Danko-Lab/TED to install (upgrade).
>
>
> *When you said "put if.vst=FALSE in the function argument", you mean
> thefunction run.Ted(..., if.vst=FALSE)?*
> yes
>
> On Mon, Jan 17, 2022 at 1:31 PM Moh Huda ***@***.***> wrote:
>
> > Dear Tinyi,
> >
> > I am currently using the RStudio server and the last time I installed
> > BayesPrism it was quite difficult and I need the admin help to resolve
the
> > issue.
> >
> > Could you please direct me to the updated version if possible?
> >
> > When you said "put if.vst=FALSE in the function argument", you mean the
> > function run.Ted(..., if.vst=FALSE)?
> >
> > I am sorry I am really bad at programming. Thank you for your help and
> > patience.
> >
> > Regards,
> >
> > Huda
> >
> > On Mon, 17 Jan 2022, 18:21 Tinyi Chu, ***@***.***> wrote:
> >
> > > Hi Huda,
> > >
> > > No, you do not need to change the code. You only need to re-install
the
> > > updated package, and put if.vst=FALSE in the function argument.
> > >
> > > Best,
> > >
> > > Tinyi
> > >
> > > On Mon, Jan 17, 2022 at 8:00 AM Moh Huda ***@***.***> wrote:
> > >
> > > > Dear Tinyi,
> > > >
> > > >
> > > > I want to confirm that the line I need to modify is line 335 from
> > > > if(if.vst){
> > > > becoming if(if.vst=FALSE){
> > > >
> > > > Is that all? Thank you very much for your help and reply.
> > > >
> > > >
> > > > Best regards,
> > > >
> > > > Huda
> > > >
> > > > On Mon, 17 Jan 2022, 07:40 Tinyi Chu, ***@***.***> wrote:
> > > >
> > > > > Hi Moh,
> > > > >
> > > > > Thank you for your question. This seems to be caused by the
sparsity
> > of
> > > > > your simulated data. If you run vst (from the DEseq2 package) on
your
> > > > > dataset, it gives the same error, which means that there are less
> > than
> > > > > 'nsub'(nsub=1000) rows with mean normalized count > 5.
> > > > >
> > > > > I added an argument of if.vst in the run.Ted function, to allow
you
> > to
> > > > > bypass the vst step. Simply set if.vst=FALSE, to disable vst.
> > > > >
> > > > > Let me know if there are any questions.
> > > > >
> > > > > Best,
> > > > >
> > > > > Tinyi
> > > > >
> > > > >
> > > > > On Sat, Jan 15, 2022 at 7:30 PM Moh Huda ***@***.***> wrote:
> > > > >
> > > > > > I have some different types of data (real data, semisynthetic
data,
> > > and
> > > > > > fully synthetic data generated using splatter software). When
> > running
> > > > the
> > > > > > data and got the message "every gene has at least one zero. vst
> > > > > > transformation is NOT feasible”, the running process is
successful.
> > > > > > However, when running different data and got the message "vst
> > > > > > transformation is feasible" the execution failed (running
process
> > > > > failed).
> > > > > > The error message is
> > > > > >
> > > > > > 1. "Error in vst(Zkg.tum.round, nsub =
min(nrow(Zkg.tum.round)/5,
> > > > > > 1000)) :
> > > > > > less than 'nsub' rows with mean normalized count > 5,
> > > > > > it is recommended to use varianceStabilizingTransformation
> > directly".
> > > > > >
> > > > > > I check the file called runTed.R and this command is in line
335.
> > The
> > > > > > suggestion there said that,
> > > > > >
> > > > > > 1. #adjust nsub, to avoid error when too few genes are used
> > > > > > What I understand that I need to change the function vst() on
the
> > > line
> > > > > > 335 to varianceStabilizingTransformation(), but it does not
work
> > > > either.
> > > > > > Also, I have no idea how to adjust nsub (the suggestion number
2
> > > > above).
> > > > > >
> > > > > > Could you please give a suggestion? Thank you.
> > > > > >
> > > > > > I attach the two sample data types.
> > > > > > rstudio-export-2.zip
> > > > > > <
> > https://github.com/Danko-Lab/TED/files/7876152/rstudio-export-2.zip
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Dear Tinyi,
Yes indeed, the argument is not in runTED yet. If successful, the argument if.vst should be there, then. However, what is the TED package version for the most updated one so that we can check if the most updated one is the one that is installed? I tried to find this information on your Github account or in the CRAN list but unfortunately I could not find it.
Thank you very much.
Regards,
Huda
run.Ted
function (ref.dat, X, cell.type.labels, cell.subtype.labels = NULL,
tum.key = NULL, input.type, pseudo.min = 1e-08, alpha = 1,
sigma = 2, outlier.cut = 0.01, outlier.fraction = 0.1, gibbs.control = list(chain.length = 1000,
burn.in = 500, thinning = 2), opt.control = list(trace = 0,
maxit = 10000), n.cores = 1, n.cores.2g = NULL, pdf.name = NULL,
first.gibbs.only = F)
{
if (is.null(colnames(ref.dat)))
stop("Error: please specify the gene names of ref.dat!")
if (is.null(colnames(X)))
stop("Error: please specify the gene names of X!")
if (is.null(cell.type.labels))
stop("Error: please specify the cell.types.labels!")
if (nrow(ref.dat) != length(cell.type.labels))
stop("Error: nrow(ref.dat) and length(cell.type.labels) need to be the same!")
if (is.null(n.cores.2g))
n.cores.2g <- n.cores
if (is.null(cell.subtype.labels))
cell.subtype.labels <- cell.type.labels
cell.type.labels <- as.character(cell.type.labels)
cell.subtype.labels <- as.character(cell.subtype.labels)
type.to.subtype.mapping <- unique(cbind(cell.type = cell.type.labels,
cell.subtype = cell.subtype.labels))
if (max(table(type.to.subtype.mapping[, "cell.subtype"])) >
1)
stop("Error: one or more subtypes belong to multiple cell types!")
if (length(unique(cell.type.labels)) > length(unique(cell.subtype.labels)))
stop("Error: more cell types than subtypes!")
print("removing non-numeric genes...")
ref.dat <- ref.dat[, apply(ref.dat, 2, function(ref.dat.gene.i) as.logical(prod(is.numeric(ref.dat.gene.i),
is.finite(ref.dat.gene.i))))]
X <- X[, apply(X, 2, function(X.gene.i) as.logical(prod(is.numeric(X.gene.i),
is.finite(X.gene.i)))), drop = F]
print("removing outlier genes...")
X.norm <- apply(X, 1, function(vec) vec/sum(vec))
filter.idx <- apply(X.norm > outlier.cut, 1, sum)/ncol(X.norm) >
outlier.fraction
X <- X[, !filter.idx, drop = F]
cat("Number of outlier genes filtered=", sum(filter.idx),
"\n")
if (!input.type %in% c("scRNA", "GEP"))
stop("Error: please specify the correct input.type!")
print("aligning reference and mixture...")
if (input.type == "GEP") {
stopifnot(nrow(ref.dat) == length(cell.type.labels))
processed.dat <- process_GEP(ref = ref.dat, mixture = X,
pseudo.min = pseudo.min, cell.type.labels = cell.type.labels)
}
if (input.type == "scRNA") {
stopifnot(nrow(ref.dat) == length(cell.subtype.labels))
processed.dat <- process_scRNA(ref = ref.dat, mixture = X,
pseudo.min = pseudo.min, cell.type.labels = cell.type.labels,
cell.subtype.labels = cell.subtype.labels)
}
if (!is.null(tum.key)) {
tum.idx <- which(rownames(processed.dat$prior.matched.norm) ==
tum.key)
if (length(tum.idx) == 0)
stop("Error: tum.key is not matched to any rownames of the reference, please check the spelling!")
processed.dat$prior.matched.norm <- processed.dat$prior.matched.norm[-tum.idx,
]
}
else print("No tumor reference is speficied. Reference profiles are treated equally.")
type.to.subtype.mapping <- type.to.subtype.mapping[match(rownames(processed.dat$ref.matched.norm),
type.to.subtype.mapping[, "cell.subtype"]), ]
rm(ref.dat, X, cell.type.labels, cell.subtype.labels)
gc()
ted.res <- run.Ted.main(input.phi = processed.dat$ref.matched.norm,
input.phi.prior = processed.dat$prior.matched.norm, X = processed.dat$mixture.matched,
tum.key = tum.key, type.to.subtype.mapping = type.to.subtype.mapping,
alpha = alpha, sigma = sigma, gibbs.control = gibbs.control,
opt.control = opt.control, n.cores = n.cores, n.cores.2g = n.cores.2g,
first.gibbs.only = first.gibbs.only)
para <- list(X = processed.dat$mixture.matched, input.phi = processed.dat$ref.matched.norm,
input.phi.prior = processed.dat$prior.matched.norm, tum.key = tum.key,
type.to.subtype.mapping = type.to.subtype.mapping, alpha = alpha,
sigma = sigma, pseudo.min = pseudo.min, gibbs.control = gibbs.control,
opt.control = opt.control, n.cores = n.cores)
ted.res$para <- para
if (!is.null(tum.key)) {
Zkg.tum <- ted.res$res$first.gibbs.res$Zkg.tum
Zkg.tum.round <- t(round(Zkg.tum))
if.vst <- sum(apply(Zkg.tum.round, 1, min) == 0) < nrow(Zkg.tum.round)
if (if.vst & nrow(Zkg.tum.round) > 1) {
print("vst transformation is feasible")
Zkg.tum.vst <- vst(Zkg.tum.round, nsub = min(nrow(Zkg.tum.round)/5,
1000))
cor.mat <- get.cormat(Zkg.tum = Zkg.tum.vst)
}
else {
if (nrow(Zkg.tum.round) == 1)
print("only one mixture sample. vst transformation is NOT feasible")
else print("every gene has at least one zero. vst transformation is NOT feasible")
Zkg.tum.vst <- NULL
cor.mat <- get.cormat(Zkg.tum = ted.res$res$first.gibbs.res$Zkg.tum.norm)
}
ted.res$res$first.gibbs.res$Zkg.tum.vst <- Zkg.tum.vst
ted.res$res$first.gibbs.res$cor.mat <- cor.mat
if (!is.null(pdf.name) & nrow(Zkg.tum.round) > 1)
plot.heatmap(dat = cor.mat, pdf.name = pdf.name,
cluster = T, self = T, show.value = F, metric = "is.cor")
}
return(ted.res)
}
<bytecode: 0x7f3c01e965c8>
<environment: namespace:TED>
… On 19 Jan 2022, at 20:56, Tinyi Chu ***@***.***> wrote:
Hi Huda,
Yes. I think you did not update the package correctly. To check, you can
simply type run.Ted in your R console, and see if the argument if.vst is in
it.
Best,
Tinyi
On Wed, Jan 19, 2022 at 3:54 PM Moh Huda ***@***.***> wrote:
> Dear Tinyi,
>
> I have updated the package TED in R and have added the argument if.vst =
> FALSE in runTED.R function This is to be precise what I have used
> run.Ted(ref.dat = filter_gene_scRNA_data, X = chosen_data, cell.type.labels
> = ***@***.***$seurat_clusters, cell.subtype.labels =
> ***@***.***$seurat_clusters, tum.key = "1", input.type = "scRNA", n.cores =
> 20, pdf.name = "tcga.tumor.synthetic", if.vst=FALSE). However, I got this
> error Error in run.Ted(ref.dat = filter_gene_scRNA_data, X = chosen_data,
> cell.type.labels = ***@***.***$seurat_clusters, :
> unused argument (if.vst = FALSE).
> 1. I suppose I use the argument incorrectly. a) Then where should this
> argument be added then? b) Or is it possible that I might fail in updating
> the package which leads to this error message?
>
> 2. The version of the package TED I got is packageVersion("TED”) [1]
> ‘1.1’. Is it the correct one for the most updated?
>
>
> Thank you very much.
>
> Regards,
>
> Huda
> > On 17 Jan 2022, at 18:36, Tinyi Chu ***@***.***> wrote:
> >
> >
> > *Could you please direct me to the updated version if possible?*
> > The github repository was updated yesterday. You may simply follow the
> > instructions on https://github.com/Danko-Lab/TED to install (upgrade).
> >
> >
> > *When you said "put if.vst=FALSE in the function argument", you mean
> > thefunction run.Ted(..., if.vst=FALSE)?*
> > yes
> >
> > On Mon, Jan 17, 2022 at 1:31 PM Moh Huda ***@***.***> wrote:
> >
> > > Dear Tinyi,
> > >
> > > I am currently using the RStudio server and the last time I installed
> > > BayesPrism it was quite difficult and I need the admin help to resolve
> the
> > > issue.
> > >
> > > Could you please direct me to the updated version if possible?
> > >
> > > When you said "put if.vst=FALSE in the function argument", you mean the
> > > function run.Ted(..., if.vst=FALSE)?
> > >
> > > I am sorry I am really bad at programming. Thank you for your help and
> > > patience.
> > >
> > > Regards,
> > >
> > > Huda
> > >
> > > On Mon, 17 Jan 2022, 18:21 Tinyi Chu, ***@***.***> wrote:
> > >
> > > > Hi Huda,
> > > >
> > > > No, you do not need to change the code. You only need to re-install
> the
> > > > updated package, and put if.vst=FALSE in the function argument.
> > > >
> > > > Best,
> > > >
> > > > Tinyi
> > > >
> > > > On Mon, Jan 17, 2022 at 8:00 AM Moh Huda ***@***.***> wrote:
> > > >
> > > > > Dear Tinyi,
> > > > >
> > > > >
> > > > > I want to confirm that the line I need to modify is line 335 from
> > > > > if(if.vst){
> > > > > becoming if(if.vst=FALSE){
> > > > >
> > > > > Is that all? Thank you very much for your help and reply.
> > > > >
> > > > >
> > > > > Best regards,
> > > > >
> > > > > Huda
> > > > >
> > > > > On Mon, 17 Jan 2022, 07:40 Tinyi Chu, ***@***.***> wrote:
> > > > >
> > > > > > Hi Moh,
> > > > > >
> > > > > > Thank you for your question. This seems to be caused by the
> sparsity
> > > of
> > > > > > your simulated data. If you run vst (from the DEseq2 package) on
> your
> > > > > > dataset, it gives the same error, which means that there are less
> > > than
> > > > > > 'nsub'(nsub=1000) rows with mean normalized count > 5.
> > > > > >
> > > > > > I added an argument of if.vst in the run.Ted function, to allow
> you
> > > to
> > > > > > bypass the vst step. Simply set if.vst=FALSE, to disable vst.
> > > > > >
> > > > > > Let me know if there are any questions.
> > > > > >
> > > > > > Best,
> > > > > >
> > > > > > Tinyi
> > > > > >
> > > > > >
> > > > > > On Sat, Jan 15, 2022 at 7:30 PM Moh Huda ***@***.***> wrote:
> > > > > >
> > > > > > > I have some different types of data (real data, semisynthetic
> data,
> > > > and
> > > > > > > fully synthetic data generated using splatter software). When
> > > running
> > > > > the
> > > > > > > data and got the message "every gene has at least one zero. vst
> > > > > > > transformation is NOT feasible”, the running process is
> successful.
> > > > > > > However, when running different data and got the message "vst
> > > > > > > transformation is feasible" the execution failed (running
> process
> > > > > > failed).
> > > > > > > The error message is
> > > > > > >
> > > > > > > 1. "Error in vst(Zkg.tum.round, nsub =
> min(nrow(Zkg.tum.round)/5,
> > > > > > > 1000)) :
> > > > > > > less than 'nsub' rows with mean normalized count > 5,
> > > > > > > it is recommended to use varianceStabilizingTransformation
> > > directly".
> > > > > > >
> > > > > > > I check the file called runTed.R and this command is in line
> 335.
> > > The
> > > > > > > suggestion there said that,
> > > > > > >
> > > > > > > 1. #adjust nsub, to avoid error when too few genes are used
> > > > > > > What I understand that I need to change the function vst() on
> the
> > > > line
> > > > > > > 335 to varianceStabilizingTransformation(), but it does not
> work
> > > > > either.
> > > > > > > Also, I have no idea how to adjust nsub (the suggestion number
> 2
> > > > > above).
> > > > > > >
> > > > > > > Could you please give a suggestion? Thank you.
> > > > > > >
> > > > > > > I attach the two sample data types.
> > > > > > > rstudio-export-2.zip
> > > > > > > <
> > > https://github.com/Danko-Lab/TED/files/7876152/rstudio-export-2.zip
> > > > >
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BayesPrism is not on CRAN yet. I did not update the version for this
update. You may simply uninstall and re-install the latest github
repository.
…On Wed, Jan 19, 2022 at 4:04 PM Moh Huda ***@***.***> wrote:
Dear Tinyi,
Yes indeed, the argument is not in runTED yet. If successful, the argument
if.vst should be there, then. However, what is the TED package version for
the most updated one so that we can check if the most updated one is the
one that is installed? I tried to find this information on your Github
account or in the CRAN list but unfortunately I could not find it.
Thank you very much.
Regards,
Huda
> run.Ted
function (ref.dat, X, cell.type.labels, cell.subtype.labels = NULL,
tum.key = NULL, input.type, pseudo.min = 1e-08, alpha = 1,
sigma = 2, outlier.cut = 0.01, outlier.fraction = 0.1, gibbs.control =
list(chain.length = 1000,
burn.in = 500, thinning = 2), opt.control = list(trace = 0,
maxit = 10000), n.cores = 1, n.cores.2g = NULL, pdf.name = NULL,
first.gibbs.only = F)
{
if (is.null(colnames(ref.dat)))
stop("Error: please specify the gene names of ref.dat!")
if (is.null(colnames(X)))
stop("Error: please specify the gene names of X!")
if (is.null(cell.type.labels))
stop("Error: please specify the cell.types.labels!")
if (nrow(ref.dat) != length(cell.type.labels))
stop("Error: nrow(ref.dat) and length(cell.type.labels) need to be the
same!")
if (is.null(n.cores.2g))
n.cores.2g <- n.cores
if (is.null(cell.subtype.labels))
cell.subtype.labels <- cell.type.labels
cell.type.labels <- as.character(cell.type.labels)
cell.subtype.labels <- as.character(cell.subtype.labels)
type.to.subtype.mapping <- unique(cbind(cell.type = cell.type.labels,
cell.subtype = cell.subtype.labels))
if (max(table(type.to.subtype.mapping[, "cell.subtype"])) >
1)
stop("Error: one or more subtypes belong to multiple cell types!")
if (length(unique(cell.type.labels)) >
length(unique(cell.subtype.labels)))
stop("Error: more cell types than subtypes!")
print("removing non-numeric genes...")
ref.dat <- ref.dat[, apply(ref.dat, 2, function(ref.dat.gene.i)
as.logical(prod(is.numeric(ref.dat.gene.i),
is.finite(ref.dat.gene.i))))]
X <- X[, apply(X, 2, function(X.gene.i)
as.logical(prod(is.numeric(X.gene.i),
is.finite(X.gene.i)))), drop = F]
print("removing outlier genes...")
X.norm <- apply(X, 1, function(vec) vec/sum(vec))
filter.idx <- apply(X.norm > outlier.cut, 1, sum)/ncol(X.norm) >
outlier.fraction
X <- X[, !filter.idx, drop = F]
cat("Number of outlier genes filtered=", sum(filter.idx),
"\n")
if (!input.type %in% c("scRNA", "GEP"))
stop("Error: please specify the correct input.type!")
print("aligning reference and mixture...")
if (input.type == "GEP") {
stopifnot(nrow(ref.dat) == length(cell.type.labels))
processed.dat <- process_GEP(ref = ref.dat, mixture = X,
pseudo.min = pseudo.min, cell.type.labels = cell.type.labels)
}
if (input.type == "scRNA") {
stopifnot(nrow(ref.dat) == length(cell.subtype.labels))
processed.dat <- process_scRNA(ref = ref.dat, mixture = X,
pseudo.min = pseudo.min, cell.type.labels = cell.type.labels,
cell.subtype.labels = cell.subtype.labels)
}
if (!is.null(tum.key)) {
tum.idx <- which(rownames(processed.dat$prior.matched.norm) ==
tum.key)
if (length(tum.idx) == 0)
stop("Error: tum.key is not matched to any rownames of the reference,
please check the spelling!")
processed.dat$prior.matched.norm <-
processed.dat$prior.matched.norm[-tum.idx,
]
}
else print("No tumor reference is speficied. Reference profiles are
treated equally.")
type.to.subtype.mapping <-
type.to.subtype.mapping[match(rownames(processed.dat$ref.matched.norm),
type.to.subtype.mapping[, "cell.subtype"]), ]
rm(ref.dat, X, cell.type.labels, cell.subtype.labels)
gc()
ted.res <- run.Ted.main(input.phi = processed.dat$ref.matched.norm,
input.phi.prior = processed.dat$prior.matched.norm, X =
processed.dat$mixture.matched,
tum.key = tum.key, type.to.subtype.mapping = type.to.subtype.mapping,
alpha = alpha, sigma = sigma, gibbs.control = gibbs.control,
opt.control = opt.control, n.cores = n.cores, n.cores.2g = n.cores.2g,
first.gibbs.only = first.gibbs.only)
para <- list(X = processed.dat$mixture.matched, input.phi =
processed.dat$ref.matched.norm,
input.phi.prior = processed.dat$prior.matched.norm, tum.key = tum.key,
type.to.subtype.mapping = type.to.subtype.mapping, alpha = alpha,
sigma = sigma, pseudo.min = pseudo.min, gibbs.control = gibbs.control,
opt.control = opt.control, n.cores = n.cores)
ted.res$para <- para
if (!is.null(tum.key)) {
Zkg.tum <- ted.res$res$first.gibbs.res$Zkg.tum
Zkg.tum.round <- t(round(Zkg.tum))
if.vst <- sum(apply(Zkg.tum.round, 1, min) == 0) < nrow(Zkg.tum.round)
if (if.vst & nrow(Zkg.tum.round) > 1) {
print("vst transformation is feasible")
Zkg.tum.vst <- vst(Zkg.tum.round, nsub = min(nrow(Zkg.tum.round)/5,
1000))
cor.mat <- get.cormat(Zkg.tum = Zkg.tum.vst)
}
else {
if (nrow(Zkg.tum.round) == 1)
print("only one mixture sample. vst transformation is NOT feasible")
else print("every gene has at least one zero. vst transformation is NOT
feasible")
Zkg.tum.vst <- NULL
cor.mat <- get.cormat(Zkg.tum = ted.res$res$first.gibbs.res$Zkg.tum.norm)
}
ted.res$res$first.gibbs.res$Zkg.tum.vst <- Zkg.tum.vst
ted.res$res$first.gibbs.res$cor.mat <- cor.mat
if (!is.null(pdf.name) & nrow(Zkg.tum.round) > 1)
plot.heatmap(dat = cor.mat, pdf.name = pdf.name,
cluster = T, self = T, show.value = F, metric = "is.cor")
}
return(ted.res)
}
<bytecode: 0x7f3c01e965c8>
<environment: namespace:TED>
> On 19 Jan 2022, at 20:56, Tinyi Chu ***@***.***> wrote:
>
>
> Hi Huda,
>
> Yes. I think you did not update the package correctly. To check, you can
> simply type run.Ted in your R console, and see if the argument if.vst is
in
> it.
>
> Best,
>
> Tinyi
>
>
>
> On Wed, Jan 19, 2022 at 3:54 PM Moh Huda ***@***.***> wrote:
>
> > Dear Tinyi,
> >
> > I have updated the package TED in R and have added the argument if.vst
=
> > FALSE in runTED.R function This is to be precise what I have used
> > run.Ted(ref.dat = filter_gene_scRNA_data, X = chosen_data,
cell.type.labels
> > = ***@***.***$seurat_clusters, cell.subtype.labels =
> > ***@***.***$seurat_clusters, tum.key = "1", input.type = "scRNA",
n.cores =
> > 20, pdf.name = "tcga.tumor.synthetic", if.vst=FALSE). However, I got
this
> > error Error in run.Ted(ref.dat = filter_gene_scRNA_data, X =
chosen_data,
> > cell.type.labels = ***@***.***$seurat_clusters, :
> > unused argument (if.vst = FALSE).
> > 1. I suppose I use the argument incorrectly. a) Then where should this
> > argument be added then? b) Or is it possible that I might fail in
updating
> > the package which leads to this error message?
> >
> > 2. The version of the package TED I got is packageVersion("TED”) [1]
> > ‘1.1’. Is it the correct one for the most updated?
> >
> >
> > Thank you very much.
> >
> > Regards,
> >
> > Huda
> > > On 17 Jan 2022, at 18:36, Tinyi Chu ***@***.***> wrote:
> > >
> > >
> > > *Could you please direct me to the updated version if possible?*
> > > The github repository was updated yesterday. You may simply follow
the
> > > instructions on https://github.com/Danko-Lab/TED to install
(upgrade).
> > >
> > >
> > > *When you said "put if.vst=FALSE in the function argument", you mean
> > > thefunction run.Ted(..., if.vst=FALSE)?*
> > > yes
> > >
> > > On Mon, Jan 17, 2022 at 1:31 PM Moh Huda ***@***.***> wrote:
> > >
> > > > Dear Tinyi,
> > > >
> > > > I am currently using the RStudio server and the last time I
installed
> > > > BayesPrism it was quite difficult and I need the admin help to
resolve
> > the
> > > > issue.
> > > >
> > > > Could you please direct me to the updated version if possible?
> > > >
> > > > When you said "put if.vst=FALSE in the function argument", you
mean the
> > > > function run.Ted(..., if.vst=FALSE)?
> > > >
> > > > I am sorry I am really bad at programming. Thank you for your help
and
> > > > patience.
> > > >
> > > > Regards,
> > > >
> > > > Huda
> > > >
> > > > On Mon, 17 Jan 2022, 18:21 Tinyi Chu, ***@***.***> wrote:
> > > >
> > > > > Hi Huda,
> > > > >
> > > > > No, you do not need to change the code. You only need to
re-install
> > the
> > > > > updated package, and put if.vst=FALSE in the function argument.
> > > > >
> > > > > Best,
> > > > >
> > > > > Tinyi
> > > > >
> > > > > On Mon, Jan 17, 2022 at 8:00 AM Moh Huda ***@***.***> wrote:
> > > > >
> > > > > > Dear Tinyi,
> > > > > >
> > > > > >
> > > > > > I want to confirm that the line I need to modify is line 335
from
> > > > > > if(if.vst){
> > > > > > becoming if(if.vst=FALSE){
> > > > > >
> > > > > > Is that all? Thank you very much for your help and reply.
> > > > > >
> > > > > >
> > > > > > Best regards,
> > > > > >
> > > > > > Huda
> > > > > >
> > > > > > On Mon, 17 Jan 2022, 07:40 Tinyi Chu, ***@***.***> wrote:
> > > > > >
> > > > > > > Hi Moh,
> > > > > > >
> > > > > > > Thank you for your question. This seems to be caused by the
> > sparsity
> > > > of
> > > > > > > your simulated data. If you run vst (from the DEseq2
package) on
> > your
> > > > > > > dataset, it gives the same error, which means that there are
less
> > > > than
> > > > > > > 'nsub'(nsub=1000) rows with mean normalized count > 5.
> > > > > > >
> > > > > > > I added an argument of if.vst in the run.Ted function, to
allow
> > you
> > > > to
> > > > > > > bypass the vst step. Simply set if.vst=FALSE, to disable vst.
> > > > > > >
> > > > > > > Let me know if there are any questions.
> > > > > > >
> > > > > > > Best,
> > > > > > >
> > > > > > > Tinyi
> > > > > > >
> > > > > > >
> > > > > > > On Sat, Jan 15, 2022 at 7:30 PM Moh Huda ***@***.***> wrote:
> > > > > > >
> > > > > > > > I have some different types of data (real data,
semisynthetic
> > data,
> > > > > and
> > > > > > > > fully synthetic data generated using splatter software).
When
> > > > running
> > > > > > the
> > > > > > > > data and got the message "every gene has at least one
zero. vst
> > > > > > > > transformation is NOT feasible”, the running process is
> > successful.
> > > > > > > > However, when running different data and got the message
"vst
> > > > > > > > transformation is feasible" the execution failed (running
> > process
> > > > > > > failed).
> > > > > > > > The error message is
> > > > > > > >
> > > > > > > > 1. "Error in vst(Zkg.tum.round, nsub =
> > min(nrow(Zkg.tum.round)/5,
> > > > > > > > 1000)) :
> > > > > > > > less than 'nsub' rows with mean normalized count > 5,
> > > > > > > > it is recommended to use varianceStabilizingTransformation
> > > > directly".
> > > > > > > >
> > > > > > > > I check the file called runTed.R and this command is in
line
> > 335.
> > > > The
> > > > > > > > suggestion there said that,
> > > > > > > >
> > > > > > > > 1. #adjust nsub, to avoid error when too few genes are used
> > > > > > > > What I understand that I need to change the function vst()
on
> > the
> > > > > line
> > > > > > > > 335 to varianceStabilizingTransformation(), but it does not
> > work
> > > > > > either.
> > > > > > > > Also, I have no idea how to adjust nsub (the suggestion
number
> > 2
> > > > > > above).
> > > > > > > >
> > > > > > > > Could you please give a suggestion? Thank you.
> > > > > > > >
> > > > > > > > I attach the two sample data types.
> > > > > > > > rstudio-export-2.zip
> > > > > > > > <
> > > >
https://github.com/Danko-Lab/TED/files/7876152/rstudio-export-2.zip
> > > > > >
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I see. Thank you very much. I will try and hopefully, it will work.
Thank you very much.
Best wishes,
Huda
… On 19 Jan 2022, at 21:58, Tinyi Chu ***@***.***> wrote:
BayesPrism is not on CRAN yet. I did not update the version for this
update. You may simply uninstall and re-install the latest github
repository.
On Wed, Jan 19, 2022 at 4:04 PM Moh Huda ***@***.***> wrote:
> Dear Tinyi,
>
> Yes indeed, the argument is not in runTED yet. If successful, the argument
> if.vst should be there, then. However, what is the TED package version for
> the most updated one so that we can check if the most updated one is the
> one that is installed? I tried to find this information on your Github
> account or in the CRAN list but unfortunately I could not find it.
>
> Thank you very much.
>
> Regards,
>
> Huda
>
> > run.Ted
> function (ref.dat, X, cell.type.labels, cell.subtype.labels = NULL,
> tum.key = NULL, input.type, pseudo.min = 1e-08, alpha = 1,
> sigma = 2, outlier.cut = 0.01, outlier.fraction = 0.1, gibbs.control =
> list(chain.length = 1000,
> burn.in = 500, thinning = 2), opt.control = list(trace = 0,
> maxit = 10000), n.cores = 1, n.cores.2g = NULL, pdf.name = NULL,
> first.gibbs.only = F)
> {
> if (is.null(colnames(ref.dat)))
> stop("Error: please specify the gene names of ref.dat!")
> if (is.null(colnames(X)))
> stop("Error: please specify the gene names of X!")
> if (is.null(cell.type.labels))
> stop("Error: please specify the cell.types.labels!")
> if (nrow(ref.dat) != length(cell.type.labels))
> stop("Error: nrow(ref.dat) and length(cell.type.labels) need to be the
> same!")
> if (is.null(n.cores.2g))
> n.cores.2g <- n.cores
> if (is.null(cell.subtype.labels))
> cell.subtype.labels <- cell.type.labels
> cell.type.labels <- as.character(cell.type.labels)
> cell.subtype.labels <- as.character(cell.subtype.labels)
> type.to.subtype.mapping <- unique(cbind(cell.type = cell.type.labels,
> cell.subtype = cell.subtype.labels))
> if (max(table(type.to.subtype.mapping[, "cell.subtype"])) >
> 1)
> stop("Error: one or more subtypes belong to multiple cell types!")
> if (length(unique(cell.type.labels)) >
> length(unique(cell.subtype.labels)))
> stop("Error: more cell types than subtypes!")
> print("removing non-numeric genes...")
> ref.dat <- ref.dat[, apply(ref.dat, 2, function(ref.dat.gene.i)
> as.logical(prod(is.numeric(ref.dat.gene.i),
> is.finite(ref.dat.gene.i))))]
> X <- X[, apply(X, 2, function(X.gene.i)
> as.logical(prod(is.numeric(X.gene.i),
> is.finite(X.gene.i)))), drop = F]
> print("removing outlier genes...")
> X.norm <- apply(X, 1, function(vec) vec/sum(vec))
> filter.idx <- apply(X.norm > outlier.cut, 1, sum)/ncol(X.norm) >
> outlier.fraction
> X <- X[, !filter.idx, drop = F]
> cat("Number of outlier genes filtered=", sum(filter.idx),
> "\n")
> if (!input.type %in% c("scRNA", "GEP"))
> stop("Error: please specify the correct input.type!")
> print("aligning reference and mixture...")
> if (input.type == "GEP") {
> stopifnot(nrow(ref.dat) == length(cell.type.labels))
> processed.dat <- process_GEP(ref = ref.dat, mixture = X,
> pseudo.min = pseudo.min, cell.type.labels = cell.type.labels)
> }
> if (input.type == "scRNA") {
> stopifnot(nrow(ref.dat) == length(cell.subtype.labels))
> processed.dat <- process_scRNA(ref = ref.dat, mixture = X,
> pseudo.min = pseudo.min, cell.type.labels = cell.type.labels,
> cell.subtype.labels = cell.subtype.labels)
> }
> if (!is.null(tum.key)) {
> tum.idx <- which(rownames(processed.dat$prior.matched.norm) ==
> tum.key)
> if (length(tum.idx) == 0)
> stop("Error: tum.key is not matched to any rownames of the reference,
> please check the spelling!")
> processed.dat$prior.matched.norm <-
> processed.dat$prior.matched.norm[-tum.idx,
> ]
> }
> else print("No tumor reference is speficied. Reference profiles are
> treated equally.")
> type.to.subtype.mapping <-
> type.to.subtype.mapping[match(rownames(processed.dat$ref.matched.norm),
> type.to.subtype.mapping[, "cell.subtype"]), ]
> rm(ref.dat, X, cell.type.labels, cell.subtype.labels)
> gc()
> ted.res <- run.Ted.main(input.phi = processed.dat$ref.matched.norm,
> input.phi.prior = processed.dat$prior.matched.norm, X =
> processed.dat$mixture.matched,
> tum.key = tum.key, type.to.subtype.mapping = type.to.subtype.mapping,
> alpha = alpha, sigma = sigma, gibbs.control = gibbs.control,
> opt.control = opt.control, n.cores = n.cores, n.cores.2g = n.cores.2g,
> first.gibbs.only = first.gibbs.only)
> para <- list(X = processed.dat$mixture.matched, input.phi =
> processed.dat$ref.matched.norm,
> input.phi.prior = processed.dat$prior.matched.norm, tum.key = tum.key,
> type.to.subtype.mapping = type.to.subtype.mapping, alpha = alpha,
> sigma = sigma, pseudo.min = pseudo.min, gibbs.control = gibbs.control,
> opt.control = opt.control, n.cores = n.cores)
> ted.res$para <- para
> if (!is.null(tum.key)) {
> Zkg.tum <- ted.res$res$first.gibbs.res$Zkg.tum
> Zkg.tum.round <- t(round(Zkg.tum))
> if.vst <- sum(apply(Zkg.tum.round, 1, min) == 0) < nrow(Zkg.tum.round)
> if (if.vst & nrow(Zkg.tum.round) > 1) {
> print("vst transformation is feasible")
> Zkg.tum.vst <- vst(Zkg.tum.round, nsub = min(nrow(Zkg.tum.round)/5,
> 1000))
> cor.mat <- get.cormat(Zkg.tum = Zkg.tum.vst)
> }
> else {
> if (nrow(Zkg.tum.round) == 1)
> print("only one mixture sample. vst transformation is NOT feasible")
> else print("every gene has at least one zero. vst transformation is NOT
> feasible")
> Zkg.tum.vst <- NULL
> cor.mat <- get.cormat(Zkg.tum = ted.res$res$first.gibbs.res$Zkg.tum.norm)
> }
> ted.res$res$first.gibbs.res$Zkg.tum.vst <- Zkg.tum.vst
> ted.res$res$first.gibbs.res$cor.mat <- cor.mat
> if (!is.null(pdf.name) & nrow(Zkg.tum.round) > 1)
> plot.heatmap(dat = cor.mat, pdf.name = pdf.name,
> cluster = T, self = T, show.value = F, metric = "is.cor")
> }
> return(ted.res)
> }
> <bytecode: 0x7f3c01e965c8>
> <environment: namespace:TED>
>
>
>
>
> > On 19 Jan 2022, at 20:56, Tinyi Chu ***@***.***> wrote:
> >
> >
> > Hi Huda,
> >
> > Yes. I think you did not update the package correctly. To check, you can
> > simply type run.Ted in your R console, and see if the argument if.vst is
> in
> > it.
> >
> > Best,
> >
> > Tinyi
> >
> >
> >
> > On Wed, Jan 19, 2022 at 3:54 PM Moh Huda ***@***.***> wrote:
> >
> > > Dear Tinyi,
> > >
> > > I have updated the package TED in R and have added the argument if.vst
> =
> > > FALSE in runTED.R function This is to be precise what I have used
> > > run.Ted(ref.dat = filter_gene_scRNA_data, X = chosen_data,
> cell.type.labels
> > > = ***@***.***$seurat_clusters, cell.subtype.labels =
> > > ***@***.***$seurat_clusters, tum.key = "1", input.type = "scRNA",
> n.cores =
> > > 20, pdf.name = "tcga.tumor.synthetic", if.vst=FALSE). However, I got
> this
> > > error Error in run.Ted(ref.dat = filter_gene_scRNA_data, X =
> chosen_data,
> > > cell.type.labels = ***@***.***$seurat_clusters, :
> > > unused argument (if.vst = FALSE).
> > > 1. I suppose I use the argument incorrectly. a) Then where should this
> > > argument be added then? b) Or is it possible that I might fail in
> updating
> > > the package which leads to this error message?
> > >
> > > 2. The version of the package TED I got is packageVersion("TED”) [1]
> > > ‘1.1’. Is it the correct one for the most updated?
> > >
> > >
> > > Thank you very much.
> > >
> > > Regards,
> > >
> > > Huda
> > > > On 17 Jan 2022, at 18:36, Tinyi Chu ***@***.***> wrote:
> > > >
> > > >
> > > > *Could you please direct me to the updated version if possible?*
> > > > The github repository was updated yesterday. You may simply follow
> the
> > > > instructions on https://github.com/Danko-Lab/TED to install
> (upgrade).
> > > >
> > > >
> > > > *When you said "put if.vst=FALSE in the function argument", you mean
> > > > thefunction run.Ted(..., if.vst=FALSE)?*
> > > > yes
> > > >
> > > > On Mon, Jan 17, 2022 at 1:31 PM Moh Huda ***@***.***> wrote:
> > > >
> > > > > Dear Tinyi,
> > > > >
> > > > > I am currently using the RStudio server and the last time I
> installed
> > > > > BayesPrism it was quite difficult and I need the admin help to
> resolve
> > > the
> > > > > issue.
> > > > >
> > > > > Could you please direct me to the updated version if possible?
> > > > >
> > > > > When you said "put if.vst=FALSE in the function argument", you
> mean the
> > > > > function run.Ted(..., if.vst=FALSE)?
> > > > >
> > > > > I am sorry I am really bad at programming. Thank you for your help
> and
> > > > > patience.
> > > > >
> > > > > Regards,
> > > > >
> > > > > Huda
> > > > >
> > > > > On Mon, 17 Jan 2022, 18:21 Tinyi Chu, ***@***.***> wrote:
> > > > >
> > > > > > Hi Huda,
> > > > > >
> > > > > > No, you do not need to change the code. You only need to
> re-install
> > > the
> > > > > > updated package, and put if.vst=FALSE in the function argument.
> > > > > >
> > > > > > Best,
> > > > > >
> > > > > > Tinyi
> > > > > >
> > > > > > On Mon, Jan 17, 2022 at 8:00 AM Moh Huda ***@***.***> wrote:
> > > > > >
> > > > > > > Dear Tinyi,
> > > > > > >
> > > > > > >
> > > > > > > I want to confirm that the line I need to modify is line 335
> from
> > > > > > > if(if.vst){
> > > > > > > becoming if(if.vst=FALSE){
> > > > > > >
> > > > > > > Is that all? Thank you very much for your help and reply.
> > > > > > >
> > > > > > >
> > > > > > > Best regards,
> > > > > > >
> > > > > > > Huda
> > > > > > >
> > > > > > > On Mon, 17 Jan 2022, 07:40 Tinyi Chu, ***@***.***> wrote:
> > > > > > >
> > > > > > > > Hi Moh,
> > > > > > > >
> > > > > > > > Thank you for your question. This seems to be caused by the
> > > sparsity
> > > > > of
> > > > > > > > your simulated data. If you run vst (from the DEseq2
> package) on
> > > your
> > > > > > > > dataset, it gives the same error, which means that there are
> less
> > > > > than
> > > > > > > > 'nsub'(nsub=1000) rows with mean normalized count > 5.
> > > > > > > >
> > > > > > > > I added an argument of if.vst in the run.Ted function, to
> allow
> > > you
> > > > > to
> > > > > > > > bypass the vst step. Simply set if.vst=FALSE, to disable vst.
> > > > > > > >
> > > > > > > > Let me know if there are any questions.
> > > > > > > >
> > > > > > > > Best,
> > > > > > > >
> > > > > > > > Tinyi
> > > > > > > >
> > > > > > > >
> > > > > > > > On Sat, Jan 15, 2022 at 7:30 PM Moh Huda ***@***.***> wrote:
> > > > > > > >
> > > > > > > > > I have some different types of data (real data,
> semisynthetic
> > > data,
> > > > > > and
> > > > > > > > > fully synthetic data generated using splatter software).
> When
> > > > > running
> > > > > > > the
> > > > > > > > > data and got the message "every gene has at least one
> zero. vst
> > > > > > > > > transformation is NOT feasible”, the running process is
> > > successful.
> > > > > > > > > However, when running different data and got the message
> "vst
> > > > > > > > > transformation is feasible" the execution failed (running
> > > process
> > > > > > > > failed).
> > > > > > > > > The error message is
> > > > > > > > >
> > > > > > > > > 1. "Error in vst(Zkg.tum.round, nsub =
> > > min(nrow(Zkg.tum.round)/5,
> > > > > > > > > 1000)) :
> > > > > > > > > less than 'nsub' rows with mean normalized count > 5,
> > > > > > > > > it is recommended to use varianceStabilizingTransformation
> > > > > directly".
> > > > > > > > >
> > > > > > > > > I check the file called runTed.R and this command is in
> line
> > > 335.
> > > > > The
> > > > > > > > > suggestion there said that,
> > > > > > > > >
> > > > > > > > > 1. #adjust nsub, to avoid error when too few genes are used
> > > > > > > > > What I understand that I need to change the function vst()
> on
> > > the
> > > > > > line
> > > > > > > > > 335 to varianceStabilizingTransformation(), but it does not
> > > work
> > > > > > > either.
> > > > > > > > > Also, I have no idea how to adjust nsub (the suggestion
> number
> > > 2
> > > > > > > above).
> > > > > > > > >
> > > > > > > > > Could you please give a suggestion? Thank you.
> > > > > > > > >
> > > > > > > > > I attach the two sample data types.
> > > > > > > > > rstudio-export-2.zip
> > > > > > > > > <
> > > > >
> https://github.com/Danko-Lab/TED/files/7876152/rstudio-export-2.zip
> > > > > > >
> > > > > > > > >
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Dear Tinyi,
I got this email from the admin for the server where I'm using the RStudio for programming.
"Dear Huda
I re-installed the package, but it still said that the installed version is the same as the github version. It refuses to uninstall though. Can you get more details from the author of how to install and uninstall?
As for the crashing problem, I think restarting r-server should fix this. I’ll need to warn those using it first.".
I experienced the R crashing last night after the admin trying to update. He suspected there is something wrong when the update was run. Could you please advise us how to uninstall and reinstall the package correctly and safely?
I really appreciate your help and understanding.
Best regards,
Huda
Get Outlook for Android<https://aka.ms/AAb9ysg>
________________________________
From: Tinyi Chu ***@***.***>
Sent: Wednesday, January 19, 2022 9:58:31 PM
To: Danko-Lab/TED ***@***.***>
Cc: Moh Huda ***@***.***>; Author ***@***.***>
Subject: Re: [Danko-Lab/TED] vst transformation is feasible, but failed executing the next command (Issue #15)
BayesPrism is not on CRAN yet. I did not update the version for this
update. You may simply uninstall and re-install the latest github
repository.
On Wed, Jan 19, 2022 at 4:04 PM Moh Huda ***@***.***> wrote:
Dear Tinyi,
Yes indeed, the argument is not in runTED yet. If successful, the argument
if.vst should be there, then. However, what is the TED package version for
the most updated one so that we can check if the most updated one is the
one that is installed? I tried to find this information on your Github
account or in the CRAN list but unfortunately I could not find it.
Thank you very much.
Regards,
Huda
> run.Ted
function (ref.dat, X, cell.type.labels, cell.subtype.labels = NULL,
tum.key = NULL, input.type, pseudo.min = 1e-08, alpha = 1,
sigma = 2, outlier.cut = 0.01, outlier.fraction = 0.1, gibbs.control =
list(chain.length = 1000,
burn.in = 500, thinning = 2), opt.control = list(trace = 0,
maxit = 10000), n.cores = 1, n.cores.2g = NULL, pdf.name = NULL,
first.gibbs.only = F)
{
if (is.null(colnames(ref.dat)))
stop("Error: please specify the gene names of ref.dat!")
if (is.null(colnames(X)))
stop("Error: please specify the gene names of X!")
if (is.null(cell.type.labels))
stop("Error: please specify the cell.types.labels!")
if (nrow(ref.dat) != length(cell.type.labels))
stop("Error: nrow(ref.dat) and length(cell.type.labels) need to be the
same!")
if (is.null(n.cores.2g))
n.cores.2g <- n.cores
if (is.null(cell.subtype.labels))
cell.subtype.labels <- cell.type.labels
cell.type.labels <- as.character(cell.type.labels)
cell.subtype.labels <- as.character(cell.subtype.labels)
type.to.subtype.mapping <- unique(cbind(cell.type = cell.type.labels,
cell.subtype = cell.subtype.labels))
if (max(table(type.to.subtype.mapping[, "cell.subtype"])) >
1)
stop("Error: one or more subtypes belong to multiple cell types!")
if (length(unique(cell.type.labels)) >
length(unique(cell.subtype.labels)))
stop("Error: more cell types than subtypes!")
print("removing non-numeric genes...")
ref.dat <- ref.dat[, apply(ref.dat, 2, function(ref.dat.gene.i)
as.logical(prod(is.numeric(ref.dat.gene.i),
is.finite(ref.dat.gene.i))))]
X <- X[, apply(X, 2, function(X.gene.i)
as.logical(prod(is.numeric(X.gene.i),
is.finite(X.gene.i)))), drop = F]
print("removing outlier genes...")
X.norm <- apply(X, 1, function(vec) vec/sum(vec))
filter.idx <- apply(X.norm > outlier.cut, 1, sum)/ncol(X.norm) >
outlier.fraction
X <- X[, !filter.idx, drop = F]
cat("Number of outlier genes filtered=", sum(filter.idx),
"\n")
if (!input.type %in% c("scRNA", "GEP"))
stop("Error: please specify the correct input.type!")
print("aligning reference and mixture...")
if (input.type == "GEP") {
stopifnot(nrow(ref.dat) == length(cell.type.labels))
processed.dat <- process_GEP(ref = ref.dat, mixture = X,
pseudo.min = pseudo.min, cell.type.labels = cell.type.labels)
}
if (input.type == "scRNA") {
stopifnot(nrow(ref.dat) == length(cell.subtype.labels))
processed.dat <- process_scRNA(ref = ref.dat, mixture = X,
pseudo.min = pseudo.min, cell.type.labels = cell.type.labels,
cell.subtype.labels = cell.subtype.labels)
}
if (!is.null(tum.key)) {
tum.idx <- which(rownames(processed.dat$prior.matched.norm) ==
tum.key)
if (length(tum.idx) == 0)
stop("Error: tum.key is not matched to any rownames of the reference,
please check the spelling!")
processed.dat$prior.matched.norm <-
processed.dat$prior.matched.norm[-tum.idx,
]
}
else print("No tumor reference is speficied. Reference profiles are
treated equally.")
type.to.subtype.mapping <-
type.to.subtype.mapping[match(rownames(processed.dat$ref.matched.norm),
type.to.subtype.mapping[, "cell.subtype"]), ]
rm(ref.dat, X, cell.type.labels, cell.subtype.labels)
gc()
ted.res <- run.Ted.main(input.phi = processed.dat$ref.matched.norm,
input.phi.prior = processed.dat$prior.matched.norm, X =
processed.dat$mixture.matched,
tum.key = tum.key, type.to.subtype.mapping = type.to.subtype.mapping,
alpha = alpha, sigma = sigma, gibbs.control = gibbs.control,
opt.control = opt.control, n.cores = n.cores, n.cores.2g = n.cores.2g,
first.gibbs.only = first.gibbs.only)
para <- list(X = processed.dat$mixture.matched, input.phi =
processed.dat$ref.matched.norm,
input.phi.prior = processed.dat$prior.matched.norm, tum.key = tum.key,
type.to.subtype.mapping = type.to.subtype.mapping, alpha = alpha,
sigma = sigma, pseudo.min = pseudo.min, gibbs.control = gibbs.control,
opt.control = opt.control, n.cores = n.cores)
ted.res$para <- para
if (!is.null(tum.key)) {
Zkg.tum <- ted.res$res$first.gibbs.res$Zkg.tum
Zkg.tum.round <- t(round(Zkg.tum))
if.vst <- sum(apply(Zkg.tum.round, 1, min) == 0) < nrow(Zkg.tum.round)
if (if.vst & nrow(Zkg.tum.round) > 1) {
print("vst transformation is feasible")
Zkg.tum.vst <- vst(Zkg.tum.round, nsub = min(nrow(Zkg.tum.round)/5,
1000))
cor.mat <- get.cormat(Zkg.tum = Zkg.tum.vst)
}
else {
if (nrow(Zkg.tum.round) == 1)
print("only one mixture sample. vst transformation is NOT feasible")
else print("every gene has at least one zero. vst transformation is NOT
feasible")
Zkg.tum.vst <- NULL
cor.mat <- get.cormat(Zkg.tum = ted.res$res$first.gibbs.res$Zkg.tum.norm)
}
ted.res$res$first.gibbs.res$Zkg.tum.vst <- Zkg.tum.vst
ted.res$res$first.gibbs.res$cor.mat <- cor.mat
if (!is.null(pdf.name) & nrow(Zkg.tum.round) > 1)
plot.heatmap(dat = cor.mat, pdf.name = pdf.name,
cluster = T, self = T, show.value = F, metric = "is.cor")
}
return(ted.res)
}
<bytecode: 0x7f3c01e965c8>
<environment: namespace:TED>
> On 19 Jan 2022, at 20:56, Tinyi Chu ***@***.***> wrote:
>
>
> Hi Huda,
>
> Yes. I think you did not update the package correctly. To check, you can
> simply type run.Ted in your R console, and see if the argument if.vst is
in
> it.
>
> Best,
>
> Tinyi
>
>
>
> On Wed, Jan 19, 2022 at 3:54 PM Moh Huda ***@***.***> wrote:
>
> > Dear Tinyi,
> >
> > I have updated the package TED in R and have added the argument if.vst
=
> > FALSE in runTED.R function This is to be precise what I have used
> > run.Ted(ref.dat = filter_gene_scRNA_data, X = chosen_data,
cell.type.labels
> > = ***@***.***$seurat_clusters, cell.subtype.labels =
> > ***@***.***$seurat_clusters, tum.key = "1", input.type = "scRNA",
n.cores =
> > 20, pdf.name = "tcga.tumor.synthetic", if.vst=FALSE). However, I got
this
> > error Error in run.Ted(ref.dat = filter_gene_scRNA_data, X =
chosen_data,
> > cell.type.labels = ***@***.***$seurat_clusters, :
> > unused argument (if.vst = FALSE).
> > 1. I suppose I use the argument incorrectly. a) Then where should this
> > argument be added then? b) Or is it possible that I might fail in
updating
> > the package which leads to this error message?
> >
> > 2. The version of the package TED I got is packageVersion("TED”) [1]
> > ‘1.1’. Is it the correct one for the most updated?
> >
> >
> > Thank you very much.
> >
> > Regards,
> >
> > Huda
> > > On 17 Jan 2022, at 18:36, Tinyi Chu ***@***.***> wrote:
> > >
> > >
> > > *Could you please direct me to the updated version if possible?*
> > > The github repository was updated yesterday. You may simply follow
the
> > > instructions on https://github.com/Danko-Lab/TED to install
(upgrade).
> > >
> > >
> > > *When you said "put if.vst=FALSE in the function argument", you mean
> > > thefunction run.Ted(..., if.vst=FALSE)?*
> > > yes
> > >
> > > On Mon, Jan 17, 2022 at 1:31 PM Moh Huda ***@***.***> wrote:
> > >
> > > > Dear Tinyi,
> > > >
> > > > I am currently using the RStudio server and the last time I
installed
> > > > BayesPrism it was quite difficult and I need the admin help to
resolve
> > the
> > > > issue.
> > > >
> > > > Could you please direct me to the updated version if possible?
> > > >
> > > > When you said "put if.vst=FALSE in the function argument", you
mean the
> > > > function run.Ted(..., if.vst=FALSE)?
> > > >
> > > > I am sorry I am really bad at programming. Thank you for your help
and
> > > > patience.
> > > >
> > > > Regards,
> > > >
> > > > Huda
> > > >
> > > > On Mon, 17 Jan 2022, 18:21 Tinyi Chu, ***@***.***> wrote:
> > > >
> > > > > Hi Huda,
> > > > >
> > > > > No, you do not need to change the code. You only need to
re-install
> > the
> > > > > updated package, and put if.vst=FALSE in the function argument.
> > > > >
> > > > > Best,
> > > > >
> > > > > Tinyi
> > > > >
> > > > > On Mon, Jan 17, 2022 at 8:00 AM Moh Huda ***@***.***> wrote:
> > > > >
> > > > > > Dear Tinyi,
> > > > > >
> > > > > >
> > > > > > I want to confirm that the line I need to modify is line 335
from
> > > > > > if(if.vst){
> > > > > > becoming if(if.vst=FALSE){
> > > > > >
> > > > > > Is that all? Thank you very much for your help and reply.
> > > > > >
> > > > > >
> > > > > > Best regards,
> > > > > >
> > > > > > Huda
> > > > > >
> > > > > > On Mon, 17 Jan 2022, 07:40 Tinyi Chu, ***@***.***> wrote:
> > > > > >
> > > > > > > Hi Moh,
> > > > > > >
> > > > > > > Thank you for your question. This seems to be caused by the
> > sparsity
> > > > of
> > > > > > > your simulated data. If you run vst (from the DEseq2
package) on
> > your
> > > > > > > dataset, it gives the same error, which means that there are
less
> > > > than
> > > > > > > 'nsub'(nsub=1000) rows with mean normalized count > 5.
> > > > > > >
> > > > > > > I added an argument of if.vst in the run.Ted function, to
allow
> > you
> > > > to
> > > > > > > bypass the vst step. Simply set if.vst=FALSE, to disable vst.
> > > > > > >
> > > > > > > Let me know if there are any questions.
> > > > > > >
> > > > > > > Best,
> > > > > > >
> > > > > > > Tinyi
> > > > > > >
> > > > > > >
> > > > > > > On Sat, Jan 15, 2022 at 7:30 PM Moh Huda ***@***.***> wrote:
> > > > > > >
> > > > > > > > I have some different types of data (real data,
semisynthetic
> > data,
> > > > > and
> > > > > > > > fully synthetic data generated using splatter software).
When
> > > > running
> > > > > > the
> > > > > > > > data and got the message "every gene has at least one
zero. vst
> > > > > > > > transformation is NOT feasible”, the running process is
> > successful.
> > > > > > > > However, when running different data and got the message
"vst
> > > > > > > > transformation is feasible" the execution failed (running
> > process
> > > > > > > failed).
> > > > > > > > The error message is
> > > > > > > >
> > > > > > > > 1. "Error in vst(Zkg.tum.round, nsub =
> > min(nrow(Zkg.tum.round)/5,
> > > > > > > > 1000)) :
> > > > > > > > less than 'nsub' rows with mean normalized count > 5,
> > > > > > > > it is recommended to use varianceStabilizingTransformation
> > > > directly".
> > > > > > > >
> > > > > > > > I check the file called runTed.R and this command is in
line
> > 335.
> > > > The
> > > > > > > > suggestion there said that,
> > > > > > > >
> > > > > > > > 1. #adjust nsub, to avoid error when too few genes are used
> > > > > > > > What I understand that I need to change the function vst()
on
> > the
> > > > > line
> > > > > > > > 335 to varianceStabilizingTransformation(), but it does not
> > work
> > > > > > either.
> > > > > > > > Also, I have no idea how to adjust nsub (the suggestion
number
> > 2
> > > > > > above).
> > > > > > > >
> > > > > > > > Could you please give a suggestion? Thank you.
> > > > > > > >
> > > > > > > > I attach the two sample data types.
> > > > > > > > rstudio-export-2.zip
> > > > > > > > <
> > > >
https://github.com/Danko-Lab/TED/files/7876152/rstudio-export-2.zip
> > > > > >
> > > > > > > >
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The installation passed tests on my side. Please simply follow standard
uninstall and installation procedures. In case it still fails, please
forward me the exact error information. Thanks.
…On Thu, Jan 20, 2022 at 5:08 AM Moh Huda ***@***.***> wrote:
Dear Tinyi,
I got this email from the admin for the server where I'm using the RStudio
for programming.
"Dear Huda
I re-installed the package, but it still said that the installed version
is the same as the github version. It refuses to uninstall though. Can you
get more details from the author of how to install and uninstall?
As for the crashing problem, I think restarting r-server should fix this.
I’ll need to warn those using it first.".
I experienced the R crashing last night after the admin trying to update.
He suspected there is something wrong when the update was run. Could you
please advise us how to uninstall and reinstall the package correctly and
safely?
I really appreciate your help and understanding.
Best regards,
Huda
Get Outlook for Android<https://aka.ms/AAb9ysg>
________________________________
From: Tinyi Chu ***@***.***>
Sent: Wednesday, January 19, 2022 9:58:31 PM
To: Danko-Lab/TED ***@***.***>
Cc: Moh Huda ***@***.***>; Author ***@***.***>
Subject: Re: [Danko-Lab/TED] vst transformation is feasible, but failed
executing the next command (Issue #15)
BayesPrism is not on CRAN yet. I did not update the version for this
update. You may simply uninstall and re-install the latest github
repository.
On Wed, Jan 19, 2022 at 4:04 PM Moh Huda ***@***.***> wrote:
> Dear Tinyi,
>
> Yes indeed, the argument is not in runTED yet. If successful, the
argument
> if.vst should be there, then. However, what is the TED package version
for
> the most updated one so that we can check if the most updated one is the
> one that is installed? I tried to find this information on your Github
> account or in the CRAN list but unfortunately I could not find it.
>
> Thank you very much.
>
> Regards,
>
> Huda
>
> > run.Ted
> function (ref.dat, X, cell.type.labels, cell.subtype.labels = NULL,
> tum.key = NULL, input.type, pseudo.min = 1e-08, alpha = 1,
> sigma = 2, outlier.cut = 0.01, outlier.fraction = 0.1, gibbs.control =
> list(chain.length = 1000,
> burn.in = 500, thinning = 2), opt.control = list(trace = 0,
> maxit = 10000), n.cores = 1, n.cores.2g = NULL, pdf.name = NULL,
> first.gibbs.only = F)
> {
> if (is.null(colnames(ref.dat)))
> stop("Error: please specify the gene names of ref.dat!")
> if (is.null(colnames(X)))
> stop("Error: please specify the gene names of X!")
> if (is.null(cell.type.labels))
> stop("Error: please specify the cell.types.labels!")
> if (nrow(ref.dat) != length(cell.type.labels))
> stop("Error: nrow(ref.dat) and length(cell.type.labels) need to be the
> same!")
> if (is.null(n.cores.2g))
> n.cores.2g <- n.cores
> if (is.null(cell.subtype.labels))
> cell.subtype.labels <- cell.type.labels
> cell.type.labels <- as.character(cell.type.labels)
> cell.subtype.labels <- as.character(cell.subtype.labels)
> type.to.subtype.mapping <- unique(cbind(cell.type = cell.type.labels,
> cell.subtype = cell.subtype.labels))
> if (max(table(type.to.subtype.mapping[, "cell.subtype"])) >
> 1)
> stop("Error: one or more subtypes belong to multiple cell types!")
> if (length(unique(cell.type.labels)) >
> length(unique(cell.subtype.labels)))
> stop("Error: more cell types than subtypes!")
> print("removing non-numeric genes...")
> ref.dat <- ref.dat[, apply(ref.dat, 2, function(ref.dat.gene.i)
> as.logical(prod(is.numeric(ref.dat.gene.i),
> is.finite(ref.dat.gene.i))))]
> X <- X[, apply(X, 2, function(X.gene.i)
> as.logical(prod(is.numeric(X.gene.i),
> is.finite(X.gene.i)))), drop = F]
> print("removing outlier genes...")
> X.norm <- apply(X, 1, function(vec) vec/sum(vec))
> filter.idx <- apply(X.norm > outlier.cut, 1, sum)/ncol(X.norm) >
> outlier.fraction
> X <- X[, !filter.idx, drop = F]
> cat("Number of outlier genes filtered=", sum(filter.idx),
> "\n")
> if (!input.type %in% c("scRNA", "GEP"))
> stop("Error: please specify the correct input.type!")
> print("aligning reference and mixture...")
> if (input.type == "GEP") {
> stopifnot(nrow(ref.dat) == length(cell.type.labels))
> processed.dat <- process_GEP(ref = ref.dat, mixture = X,
> pseudo.min = pseudo.min, cell.type.labels = cell.type.labels)
> }
> if (input.type == "scRNA") {
> stopifnot(nrow(ref.dat) == length(cell.subtype.labels))
> processed.dat <- process_scRNA(ref = ref.dat, mixture = X,
> pseudo.min = pseudo.min, cell.type.labels = cell.type.labels,
> cell.subtype.labels = cell.subtype.labels)
> }
> if (!is.null(tum.key)) {
> tum.idx <- which(rownames(processed.dat$prior.matched.norm) ==
> tum.key)
> if (length(tum.idx) == 0)
> stop("Error: tum.key is not matched to any rownames of the reference,
> please check the spelling!")
> processed.dat$prior.matched.norm <-
> processed.dat$prior.matched.norm[-tum.idx,
> ]
> }
> else print("No tumor reference is speficied. Reference profiles are
> treated equally.")
> type.to.subtype.mapping <-
> type.to.subtype.mapping[match(rownames(processed.dat$ref.matched.norm),
> type.to.subtype.mapping[, "cell.subtype"]), ]
> rm(ref.dat, X, cell.type.labels, cell.subtype.labels)
> gc()
> ted.res <- run.Ted.main(input.phi = processed.dat$ref.matched.norm,
> input.phi.prior = processed.dat$prior.matched.norm, X =
> processed.dat$mixture.matched,
> tum.key = tum.key, type.to.subtype.mapping = type.to.subtype.mapping,
> alpha = alpha, sigma = sigma, gibbs.control = gibbs.control,
> opt.control = opt.control, n.cores = n.cores, n.cores.2g = n.cores.2g,
> first.gibbs.only = first.gibbs.only)
> para <- list(X = processed.dat$mixture.matched, input.phi =
> processed.dat$ref.matched.norm,
> input.phi.prior = processed.dat$prior.matched.norm, tum.key = tum.key,
> type.to.subtype.mapping = type.to.subtype.mapping, alpha = alpha,
> sigma = sigma, pseudo.min = pseudo.min, gibbs.control = gibbs.control,
> opt.control = opt.control, n.cores = n.cores)
> ted.res$para <- para
> if (!is.null(tum.key)) {
> Zkg.tum <- ted.res$res$first.gibbs.res$Zkg.tum
> Zkg.tum.round <- t(round(Zkg.tum))
> if.vst <- sum(apply(Zkg.tum.round, 1, min) == 0) < nrow(Zkg.tum.round)
> if (if.vst & nrow(Zkg.tum.round) > 1) {
> print("vst transformation is feasible")
> Zkg.tum.vst <- vst(Zkg.tum.round, nsub = min(nrow(Zkg.tum.round)/5,
> 1000))
> cor.mat <- get.cormat(Zkg.tum = Zkg.tum.vst)
> }
> else {
> if (nrow(Zkg.tum.round) == 1)
> print("only one mixture sample. vst transformation is NOT feasible")
> else print("every gene has at least one zero. vst transformation is NOT
> feasible")
> Zkg.tum.vst <- NULL
> cor.mat <- get.cormat(Zkg.tum = ted.res$res$first.gibbs.res$Zkg.tum.norm)
> }
> ted.res$res$first.gibbs.res$Zkg.tum.vst <- Zkg.tum.vst
> ted.res$res$first.gibbs.res$cor.mat <- cor.mat
> if (!is.null(pdf.name) & nrow(Zkg.tum.round) > 1)
> plot.heatmap(dat = cor.mat, pdf.name = pdf.name,
> cluster = T, self = T, show.value = F, metric = "is.cor")
> }
> return(ted.res)
> }
> <bytecode: 0x7f3c01e965c8>
> <environment: namespace:TED>
>
>
>
>
> > On 19 Jan 2022, at 20:56, Tinyi Chu ***@***.***> wrote:
> >
> >
> > Hi Huda,
> >
> > Yes. I think you did not update the package correctly. To check, you
can
> > simply type run.Ted in your R console, and see if the argument if.vst
is
> in
> > it.
> >
> > Best,
> >
> > Tinyi
> >
> >
> >
> > On Wed, Jan 19, 2022 at 3:54 PM Moh Huda ***@***.***> wrote:
> >
> > > Dear Tinyi,
> > >
> > > I have updated the package TED in R and have added the argument
if.vst
> =
> > > FALSE in runTED.R function This is to be precise what I have used
> > > run.Ted(ref.dat = filter_gene_scRNA_data, X = chosen_data,
> cell.type.labels
> > > = ***@***.***$seurat_clusters, cell.subtype.labels =
> > > ***@***.***$seurat_clusters, tum.key = "1", input.type = "scRNA",
> n.cores =
> > > 20, pdf.name = "tcga.tumor.synthetic", if.vst=FALSE). However, I got
> this
> > > error Error in run.Ted(ref.dat = filter_gene_scRNA_data, X =
> chosen_data,
> > > cell.type.labels = ***@***.***$seurat_clusters, :
> > > unused argument (if.vst = FALSE).
> > > 1. I suppose I use the argument incorrectly. a) Then where should
this
> > > argument be added then? b) Or is it possible that I might fail in
> updating
> > > the package which leads to this error message?
> > >
> > > 2. The version of the package TED I got is packageVersion("TED”) [1]
> > > ‘1.1’. Is it the correct one for the most updated?
> > >
> > >
> > > Thank you very much.
> > >
> > > Regards,
> > >
> > > Huda
> > > > On 17 Jan 2022, at 18:36, Tinyi Chu ***@***.***> wrote:
> > > >
> > > >
> > > > *Could you please direct me to the updated version if possible?*
> > > > The github repository was updated yesterday. You may simply follow
> the
> > > > instructions on https://github.com/Danko-Lab/TED to install
> (upgrade).
> > > >
> > > >
> > > > *When you said "put if.vst=FALSE in the function argument", you
mean
> > > > thefunction run.Ted(..., if.vst=FALSE)?*
> > > > yes
> > > >
> > > > On Mon, Jan 17, 2022 at 1:31 PM Moh Huda ***@***.***> wrote:
> > > >
> > > > > Dear Tinyi,
> > > > >
> > > > > I am currently using the RStudio server and the last time I
> installed
> > > > > BayesPrism it was quite difficult and I need the admin help to
> resolve
> > > the
> > > > > issue.
> > > > >
> > > > > Could you please direct me to the updated version if possible?
> > > > >
> > > > > When you said "put if.vst=FALSE in the function argument", you
> mean the
> > > > > function run.Ted(..., if.vst=FALSE)?
> > > > >
> > > > > I am sorry I am really bad at programming. Thank you for your
help
> and
> > > > > patience.
> > > > >
> > > > > Regards,
> > > > >
> > > > > Huda
> > > > >
> > > > > On Mon, 17 Jan 2022, 18:21 Tinyi Chu, ***@***.***> wrote:
> > > > >
> > > > > > Hi Huda,
> > > > > >
> > > > > > No, you do not need to change the code. You only need to
> re-install
> > > the
> > > > > > updated package, and put if.vst=FALSE in the function argument.
> > > > > >
> > > > > > Best,
> > > > > >
> > > > > > Tinyi
> > > > > >
> > > > > > On Mon, Jan 17, 2022 at 8:00 AM Moh Huda ***@***.***> wrote:
> > > > > >
> > > > > > > Dear Tinyi,
> > > > > > >
> > > > > > >
> > > > > > > I want to confirm that the line I need to modify is line 335
> from
> > > > > > > if(if.vst){
> > > > > > > becoming if(if.vst=FALSE){
> > > > > > >
> > > > > > > Is that all? Thank you very much for your help and reply.
> > > > > > >
> > > > > > >
> > > > > > > Best regards,
> > > > > > >
> > > > > > > Huda
> > > > > > >
> > > > > > > On Mon, 17 Jan 2022, 07:40 Tinyi Chu, ***@***.***> wrote:
> > > > > > >
> > > > > > > > Hi Moh,
> > > > > > > >
> > > > > > > > Thank you for your question. This seems to be caused by the
> > > sparsity
> > > > > of
> > > > > > > > your simulated data. If you run vst (from the DEseq2
> package) on
> > > your
> > > > > > > > dataset, it gives the same error, which means that there
are
> less
> > > > > than
> > > > > > > > 'nsub'(nsub=1000) rows with mean normalized count > 5.
> > > > > > > >
> > > > > > > > I added an argument of if.vst in the run.Ted function, to
> allow
> > > you
> > > > > to
> > > > > > > > bypass the vst step. Simply set if.vst=FALSE, to disable
vst.
> > > > > > > >
> > > > > > > > Let me know if there are any questions.
> > > > > > > >
> > > > > > > > Best,
> > > > > > > >
> > > > > > > > Tinyi
> > > > > > > >
> > > > > > > >
> > > > > > > > On Sat, Jan 15, 2022 at 7:30 PM Moh Huda ***@***.***>
wrote:
> > > > > > > >
> > > > > > > > > I have some different types of data (real data,
> semisynthetic
> > > data,
> > > > > > and
> > > > > > > > > fully synthetic data generated using splatter software).
> When
> > > > > running
> > > > > > > the
> > > > > > > > > data and got the message "every gene has at least one
> zero. vst
> > > > > > > > > transformation is NOT feasible”, the running process is
> > > successful.
> > > > > > > > > However, when running different data and got the message
> "vst
> > > > > > > > > transformation is feasible" the execution failed (running
> > > process
> > > > > > > > failed).
> > > > > > > > > The error message is
> > > > > > > > >
> > > > > > > > > 1. "Error in vst(Zkg.tum.round, nsub =
> > > min(nrow(Zkg.tum.round)/5,
> > > > > > > > > 1000)) :
> > > > > > > > > less than 'nsub' rows with mean normalized count > 5,
> > > > > > > > > it is recommended to use
varianceStabilizingTransformation
> > > > > directly".
> > > > > > > > >
> > > > > > > > > I check the file called runTed.R and this command is in
> line
> > > 335.
> > > > > The
> > > > > > > > > suggestion there said that,
> > > > > > > > >
> > > > > > > > > 1. #adjust nsub, to avoid error when too few genes are
used
> > > > > > > > > What I understand that I need to change the function
vst()
> on
> > > the
> > > > > > line
> > > > > > > > > 335 to varianceStabilizingTransformation(), but it does
not
> > > work
> > > > > > > either.
> > > > > > > > > Also, I have no idea how to adjust nsub (the suggestion
> number
> > > 2
> > > > > > > above).
> > > > > > > > >
> > > > > > > > > Could you please give a suggestion? Thank you.
> > > > > > > > >
> > > > > > > > > I attach the two sample data types.
> > > > > > > > > rstudio-export-2.zip
> > > > > > > > > <
> > > > >
> https://github.com/Danko-Lab/TED/files/7876152/rstudio-export-2.zip
> > > > > > >
> > > > > > > > >
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Dear Tinyi,
I got the update from the admin. The message is
"I tired installing again from github, and this time there was no error
message saying that the github version was the same as that already
installed. I guess an old version was cached somewhere, but you now have
the latest release so hopefully this will work."
Although the admin said it is successful, when I checked the runTed.R
function, it still has the old function behaviour (without if.vst =
FALSE). I had load the package using library(TED), then run the function
runTed.R and as expected it was error saying "unused argument (if.vst =
False).
The version I got package.version("TED") is 1.1. Could you please advise
what might be the problem?
Thank you very much for your help.
Best regards,
Huda
…On Thu, 20 Jan 2022, 15:32 Tinyi Chu, ***@***.***> wrote:
The installation passed tests on my side. Please simply follow standard
uninstall and installation procedures. In case it still fails, please
forward me the exact error information. Thanks.
On Thu, Jan 20, 2022 at 5:08 AM Moh Huda ***@***.***> wrote:
> Dear Tinyi,
>
> I got this email from the admin for the server where I'm using the
RStudio
> for programming.
>
>
> "Dear Huda
>
>
>
> I re-installed the package, but it still said that the installed version
> is the same as the github version. It refuses to uninstall though. Can
you
> get more details from the author of how to install and uninstall?
>
>
>
> As for the crashing problem, I think restarting r-server should fix this.
> I’ll need to warn those using it first.".
>
>
> I experienced the R crashing last night after the admin trying to update.
> He suspected there is something wrong when the update was run. Could you
> please advise us how to uninstall and reinstall the package correctly and
> safely?
>
>
> I really appreciate your help and understanding.
>
>
>
> Best regards,
>
>
> Huda
>
>
>
> Get Outlook for Android<https://aka.ms/AAb9ysg>
> ________________________________
> From: Tinyi Chu ***@***.***>
> Sent: Wednesday, January 19, 2022 9:58:31 PM
> To: Danko-Lab/TED ***@***.***>
> Cc: Moh Huda ***@***.***>; Author ***@***.***>
> Subject: Re: [Danko-Lab/TED] vst transformation is feasible, but failed
> executing the next command (Issue #15)
>
>
> BayesPrism is not on CRAN yet. I did not update the version for this
> update. You may simply uninstall and re-install the latest github
> repository.
>
> On Wed, Jan 19, 2022 at 4:04 PM Moh Huda ***@***.***> wrote:
>
> > Dear Tinyi,
> >
> > Yes indeed, the argument is not in runTED yet. If successful, the
> argument
> > if.vst should be there, then. However, what is the TED package version
> for
> > the most updated one so that we can check if the most updated one is
the
> > one that is installed? I tried to find this information on your Github
> > account or in the CRAN list but unfortunately I could not find it.
> >
> > Thank you very much.
> >
> > Regards,
> >
> > Huda
> >
> > > run.Ted
> > function (ref.dat, X, cell.type.labels, cell.subtype.labels = NULL,
> > tum.key = NULL, input.type, pseudo.min = 1e-08, alpha = 1,
> > sigma = 2, outlier.cut = 0.01, outlier.fraction = 0.1, gibbs.control =
> > list(chain.length = 1000,
> > burn.in = 500, thinning = 2), opt.control = list(trace = 0,
> > maxit = 10000), n.cores = 1, n.cores.2g = NULL, pdf.name = NULL,
> > first.gibbs.only = F)
> > {
> > if (is.null(colnames(ref.dat)))
> > stop("Error: please specify the gene names of ref.dat!")
> > if (is.null(colnames(X)))
> > stop("Error: please specify the gene names of X!")
> > if (is.null(cell.type.labels))
> > stop("Error: please specify the cell.types.labels!")
> > if (nrow(ref.dat) != length(cell.type.labels))
> > stop("Error: nrow(ref.dat) and length(cell.type.labels) need to be the
> > same!")
> > if (is.null(n.cores.2g))
> > n.cores.2g <- n.cores
> > if (is.null(cell.subtype.labels))
> > cell.subtype.labels <- cell.type.labels
> > cell.type.labels <- as.character(cell.type.labels)
> > cell.subtype.labels <- as.character(cell.subtype.labels)
> > type.to.subtype.mapping <- unique(cbind(cell.type = cell.type.labels,
> > cell.subtype = cell.subtype.labels))
> > if (max(table(type.to.subtype.mapping[, "cell.subtype"])) >
> > 1)
> > stop("Error: one or more subtypes belong to multiple cell types!")
> > if (length(unique(cell.type.labels)) >
> > length(unique(cell.subtype.labels)))
> > stop("Error: more cell types than subtypes!")
> > print("removing non-numeric genes...")
> > ref.dat <- ref.dat[, apply(ref.dat, 2, function(ref.dat.gene.i)
> > as.logical(prod(is.numeric(ref.dat.gene.i),
> > is.finite(ref.dat.gene.i))))]
> > X <- X[, apply(X, 2, function(X.gene.i)
> > as.logical(prod(is.numeric(X.gene.i),
> > is.finite(X.gene.i)))), drop = F]
> > print("removing outlier genes...")
> > X.norm <- apply(X, 1, function(vec) vec/sum(vec))
> > filter.idx <- apply(X.norm > outlier.cut, 1, sum)/ncol(X.norm) >
> > outlier.fraction
> > X <- X[, !filter.idx, drop = F]
> > cat("Number of outlier genes filtered=", sum(filter.idx),
> > "\n")
> > if (!input.type %in% c("scRNA", "GEP"))
> > stop("Error: please specify the correct input.type!")
> > print("aligning reference and mixture...")
> > if (input.type == "GEP") {
> > stopifnot(nrow(ref.dat) == length(cell.type.labels))
> > processed.dat <- process_GEP(ref = ref.dat, mixture = X,
> > pseudo.min = pseudo.min, cell.type.labels = cell.type.labels)
> > }
> > if (input.type == "scRNA") {
> > stopifnot(nrow(ref.dat) == length(cell.subtype.labels))
> > processed.dat <- process_scRNA(ref = ref.dat, mixture = X,
> > pseudo.min = pseudo.min, cell.type.labels = cell.type.labels,
> > cell.subtype.labels = cell.subtype.labels)
> > }
> > if (!is.null(tum.key)) {
> > tum.idx <- which(rownames(processed.dat$prior.matched.norm) ==
> > tum.key)
> > if (length(tum.idx) == 0)
> > stop("Error: tum.key is not matched to any rownames of the reference,
> > please check the spelling!")
> > processed.dat$prior.matched.norm <-
> > processed.dat$prior.matched.norm[-tum.idx,
> > ]
> > }
> > else print("No tumor reference is speficied. Reference profiles are
> > treated equally.")
> > type.to.subtype.mapping <-
> > type.to.subtype.mapping[match(rownames(processed.dat$ref.matched.norm),
> > type.to.subtype.mapping[, "cell.subtype"]), ]
> > rm(ref.dat, X, cell.type.labels, cell.subtype.labels)
> > gc()
> > ted.res <- run.Ted.main(input.phi = processed.dat$ref.matched.norm,
> > input.phi.prior = processed.dat$prior.matched.norm, X =
> > processed.dat$mixture.matched,
> > tum.key = tum.key, type.to.subtype.mapping = type.to.subtype.mapping,
> > alpha = alpha, sigma = sigma, gibbs.control = gibbs.control,
> > opt.control = opt.control, n.cores = n.cores, n.cores.2g = n.cores.2g,
> > first.gibbs.only = first.gibbs.only)
> > para <- list(X = processed.dat$mixture.matched, input.phi =
> > processed.dat$ref.matched.norm,
> > input.phi.prior = processed.dat$prior.matched.norm, tum.key = tum.key,
> > type.to.subtype.mapping = type.to.subtype.mapping, alpha = alpha,
> > sigma = sigma, pseudo.min = pseudo.min, gibbs.control = gibbs.control,
> > opt.control = opt.control, n.cores = n.cores)
> > ted.res$para <- para
> > if (!is.null(tum.key)) {
> > Zkg.tum <- ted.res$res$first.gibbs.res$Zkg.tum
> > Zkg.tum.round <- t(round(Zkg.tum))
> > if.vst <- sum(apply(Zkg.tum.round, 1, min) == 0) < nrow(Zkg.tum.round)
> > if (if.vst & nrow(Zkg.tum.round) > 1) {
> > print("vst transformation is feasible")
> > Zkg.tum.vst <- vst(Zkg.tum.round, nsub = min(nrow(Zkg.tum.round)/5,
> > 1000))
> > cor.mat <- get.cormat(Zkg.tum = Zkg.tum.vst)
> > }
> > else {
> > if (nrow(Zkg.tum.round) == 1)
> > print("only one mixture sample. vst transformation is NOT feasible")
> > else print("every gene has at least one zero. vst transformation is NOT
> > feasible")
> > Zkg.tum.vst <- NULL
> > cor.mat <- get.cormat(Zkg.tum =
ted.res$res$first.gibbs.res$Zkg.tum.norm)
> > }
> > ted.res$res$first.gibbs.res$Zkg.tum.vst <- Zkg.tum.vst
> > ted.res$res$first.gibbs.res$cor.mat <- cor.mat
> > if (!is.null(pdf.name) & nrow(Zkg.tum.round) > 1)
> > plot.heatmap(dat = cor.mat, pdf.name = pdf.name,
> > cluster = T, self = T, show.value = F, metric = "is.cor")
> > }
> > return(ted.res)
> > }
> > <bytecode: 0x7f3c01e965c8>
> > <environment: namespace:TED>
> >
> >
> >
> >
> > > On 19 Jan 2022, at 20:56, Tinyi Chu ***@***.***> wrote:
> > >
> > >
> > > Hi Huda,
> > >
> > > Yes. I think you did not update the package correctly. To check, you
> can
> > > simply type run.Ted in your R console, and see if the argument if.vst
> is
> > in
> > > it.
> > >
> > > Best,
> > >
> > > Tinyi
> > >
> > >
> > >
> > > On Wed, Jan 19, 2022 at 3:54 PM Moh Huda ***@***.***> wrote:
> > >
> > > > Dear Tinyi,
> > > >
> > > > I have updated the package TED in R and have added the argument
> if.vst
> > =
> > > > FALSE in runTED.R function This is to be precise what I have used
> > > > run.Ted(ref.dat = filter_gene_scRNA_data, X = chosen_data,
> > cell.type.labels
> > > > = ***@***.***$seurat_clusters, cell.subtype.labels =
> > > > ***@***.***$seurat_clusters, tum.key = "1", input.type = "scRNA",
> > n.cores =
> > > > 20, pdf.name = "tcga.tumor.synthetic", if.vst=FALSE). However, I
got
> > this
> > > > error Error in run.Ted(ref.dat = filter_gene_scRNA_data, X =
> > chosen_data,
> > > > cell.type.labels = ***@***.***$seurat_clusters, :
> > > > unused argument (if.vst = FALSE).
> > > > 1. I suppose I use the argument incorrectly. a) Then where should
> this
> > > > argument be added then? b) Or is it possible that I might fail in
> > updating
> > > > the package which leads to this error message?
> > > >
> > > > 2. The version of the package TED I got is packageVersion("TED”)
[1]
> > > > ‘1.1’. Is it the correct one for the most updated?
> > > >
> > > >
> > > > Thank you very much.
> > > >
> > > > Regards,
> > > >
> > > > Huda
> > > > > On 17 Jan 2022, at 18:36, Tinyi Chu ***@***.***> wrote:
> > > > >
> > > > >
> > > > > *Could you please direct me to the updated version if possible?*
> > > > > The github repository was updated yesterday. You may simply
follow
> > the
> > > > > instructions on https://github.com/Danko-Lab/TED to install
> > (upgrade).
> > > > >
> > > > >
> > > > > *When you said "put if.vst=FALSE in the function argument", you
> mean
> > > > > thefunction run.Ted(..., if.vst=FALSE)?*
> > > > > yes
> > > > >
> > > > > On Mon, Jan 17, 2022 at 1:31 PM Moh Huda ***@***.***> wrote:
> > > > >
> > > > > > Dear Tinyi,
> > > > > >
> > > > > > I am currently using the RStudio server and the last time I
> > installed
> > > > > > BayesPrism it was quite difficult and I need the admin help to
> > resolve
> > > > the
> > > > > > issue.
> > > > > >
> > > > > > Could you please direct me to the updated version if possible?
> > > > > >
> > > > > > When you said "put if.vst=FALSE in the function argument", you
> > mean the
> > > > > > function run.Ted(..., if.vst=FALSE)?
> > > > > >
> > > > > > I am sorry I am really bad at programming. Thank you for your
> help
> > and
> > > > > > patience.
> > > > > >
> > > > > > Regards,
> > > > > >
> > > > > > Huda
> > > > > >
> > > > > > On Mon, 17 Jan 2022, 18:21 Tinyi Chu, ***@***.***> wrote:
> > > > > >
> > > > > > > Hi Huda,
> > > > > > >
> > > > > > > No, you do not need to change the code. You only need to
> > re-install
> > > > the
> > > > > > > updated package, and put if.vst=FALSE in the function
argument.
> > > > > > >
> > > > > > > Best,
> > > > > > >
> > > > > > > Tinyi
> > > > > > >
> > > > > > > On Mon, Jan 17, 2022 at 8:00 AM Moh Huda ***@***.***> wrote:
> > > > > > >
> > > > > > > > Dear Tinyi,
> > > > > > > >
> > > > > > > >
> > > > > > > > I want to confirm that the line I need to modify is line
335
> > from
> > > > > > > > if(if.vst){
> > > > > > > > becoming if(if.vst=FALSE){
> > > > > > > >
> > > > > > > > Is that all? Thank you very much for your help and reply.
> > > > > > > >
> > > > > > > >
> > > > > > > > Best regards,
> > > > > > > >
> > > > > > > > Huda
> > > > > > > >
> > > > > > > > On Mon, 17 Jan 2022, 07:40 Tinyi Chu, ***@***.***> wrote:
> > > > > > > >
> > > > > > > > > Hi Moh,
> > > > > > > > >
> > > > > > > > > Thank you for your question. This seems to be caused by
the
> > > > sparsity
> > > > > > of
> > > > > > > > > your simulated data. If you run vst (from the DEseq2
> > package) on
> > > > your
> > > > > > > > > dataset, it gives the same error, which means that there
> are
> > less
> > > > > > than
> > > > > > > > > 'nsub'(nsub=1000) rows with mean normalized count > 5.
> > > > > > > > >
> > > > > > > > > I added an argument of if.vst in the run.Ted function, to
> > allow
> > > > you
> > > > > > to
> > > > > > > > > bypass the vst step. Simply set if.vst=FALSE, to disable
> vst.
> > > > > > > > >
> > > > > > > > > Let me know if there are any questions.
> > > > > > > > >
> > > > > > > > > Best,
> > > > > > > > >
> > > > > > > > > Tinyi
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > On Sat, Jan 15, 2022 at 7:30 PM Moh Huda ***@***.***>
> wrote:
> > > > > > > > >
> > > > > > > > > > I have some different types of data (real data,
> > semisynthetic
> > > > data,
> > > > > > > and
> > > > > > > > > > fully synthetic data generated using splatter
software).
> > When
> > > > > > running
> > > > > > > > the
> > > > > > > > > > data and got the message "every gene has at least one
> > zero. vst
> > > > > > > > > > transformation is NOT feasible”, the running process is
> > > > successful.
> > > > > > > > > > However, when running different data and got the
message
> > "vst
> > > > > > > > > > transformation is feasible" the execution failed
(running
> > > > process
> > > > > > > > > failed).
> > > > > > > > > > The error message is
> > > > > > > > > >
> > > > > > > > > > 1. "Error in vst(Zkg.tum.round, nsub =
> > > > min(nrow(Zkg.tum.round)/5,
> > > > > > > > > > 1000)) :
> > > > > > > > > > less than 'nsub' rows with mean normalized count > 5,
> > > > > > > > > > it is recommended to use
> varianceStabilizingTransformation
> > > > > > directly".
> > > > > > > > > >
> > > > > > > > > > I check the file called runTed.R and this command is in
> > line
> > > > 335.
> > > > > > The
> > > > > > > > > > suggestion there said that,
> > > > > > > > > >
> > > > > > > > > > 1. #adjust nsub, to avoid error when too few genes are
> used
> > > > > > > > > > What I understand that I need to change the function
> vst()
> > on
> > > > the
> > > > > > > line
> > > > > > > > > > 335 to varianceStabilizingTransformation(), but it does
> not
> > > > work
> > > > > > > > either.
> > > > > > > > > > Also, I have no idea how to adjust nsub (the suggestion
> > number
> > > > 2
> > > > > > > > above).
> > > > > > > > > >
> > > > > > > > > > Could you please give a suggestion? Thank you.
> > > > > > > > > >
> > > > > > > > > > I attach the two sample data types.
> > > > > > > > > > rstudio-export-2.zip
> > > > > > > > > > <
> > > > > >
> > https://github.com/Danko-Lab/TED/files/7876152/rstudio-export-2.zip
> > > > > > > >
> > > > > > > > > >
> > > > > > > > > > —
> > > > > > > > > > Reply to this email directly, view it on GitHub
> > > > > > > > > > <#15>, or
> > unsubscribe
> > > > > > > > > > <
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> > > > > > >
> > > > > >
> > > >
> >
>
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> > > > > > > > > > .
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> > > > > > > > > >.
> > > > > > > > > >
> > > > > > > > > > You are receiving this because you are subscribed to
this
> > > > > > > > thread.Message
> > > > > > > > > > ID: ***@***.***>
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please do a uninstall and re-install.
…On Thu, Jan 20, 2022 at 3:01 PM Moh Huda ***@***.***> wrote:
Dear Tinyi,
I got the update from the admin. The message is
"I tired installing again from github, and this time there was no error
message saying that the github version was the same as that already
installed. I guess an old version was cached somewhere, but you now have
the latest release so hopefully this will work."
Although the admin said it is successful, when I checked the runTed.R
function, it still has the old function behaviour (without if.vst =
FALSE). I had load the package using library(TED), then run the function
runTed.R and as expected it was error saying "unused argument (if.vst =
False).
The version I got package.version("TED") is 1.1. Could you please advise
what might be the problem?
Thank you very much for your help.
Best regards,
Huda
On Thu, 20 Jan 2022, 15:32 Tinyi Chu, ***@***.***> wrote:
> The installation passed tests on my side. Please simply follow standard
> uninstall and installation procedures. In case it still fails, please
> forward me the exact error information. Thanks.
>
> On Thu, Jan 20, 2022 at 5:08 AM Moh Huda ***@***.***> wrote:
>
> > Dear Tinyi,
> >
> > I got this email from the admin for the server where I'm using the
> RStudio
> > for programming.
> >
> >
> > "Dear Huda
> >
> >
> >
> > I re-installed the package, but it still said that the installed
version
> > is the same as the github version. It refuses to uninstall though. Can
> you
> > get more details from the author of how to install and uninstall?
> >
> >
> >
> > As for the crashing problem, I think restarting r-server should fix
this.
> > I’ll need to warn those using it first.".
> >
> >
> > I experienced the R crashing last night after the admin trying to
update.
> > He suspected there is something wrong when the update was run. Could
you
> > please advise us how to uninstall and reinstall the package correctly
and
> > safely?
> >
> >
> > I really appreciate your help and understanding.
> >
> >
> >
> > Best regards,
> >
> >
> > Huda
> >
> >
> >
> > Get Outlook for Android<https://aka.ms/AAb9ysg>
> > ________________________________
> > From: Tinyi Chu ***@***.***>
> > Sent: Wednesday, January 19, 2022 9:58:31 PM
> > To: Danko-Lab/TED ***@***.***>
> > Cc: Moh Huda ***@***.***>; Author ***@***.***>
> > Subject: Re: [Danko-Lab/TED] vst transformation is feasible, but failed
> > executing the next command (Issue #15)
> >
> >
> > BayesPrism is not on CRAN yet. I did not update the version for this
> > update. You may simply uninstall and re-install the latest github
> > repository.
> >
> > On Wed, Jan 19, 2022 at 4:04 PM Moh Huda ***@***.***> wrote:
> >
> > > Dear Tinyi,
> > >
> > > Yes indeed, the argument is not in runTED yet. If successful, the
> > argument
> > > if.vst should be there, then. However, what is the TED package
version
> > for
> > > the most updated one so that we can check if the most updated one is
> the
> > > one that is installed? I tried to find this information on your
Github
> > > account or in the CRAN list but unfortunately I could not find it.
> > >
> > > Thank you very much.
> > >
> > > Regards,
> > >
> > > Huda
> > >
> > > > run.Ted
> > > function (ref.dat, X, cell.type.labels, cell.subtype.labels = NULL,
> > > tum.key = NULL, input.type, pseudo.min = 1e-08, alpha = 1,
> > > sigma = 2, outlier.cut = 0.01, outlier.fraction = 0.1, gibbs.control
=
> > > list(chain.length = 1000,
> > > burn.in = 500, thinning = 2), opt.control = list(trace = 0,
> > > maxit = 10000), n.cores = 1, n.cores.2g = NULL, pdf.name = NULL,
> > > first.gibbs.only = F)
> > > {
> > > if (is.null(colnames(ref.dat)))
> > > stop("Error: please specify the gene names of ref.dat!")
> > > if (is.null(colnames(X)))
> > > stop("Error: please specify the gene names of X!")
> > > if (is.null(cell.type.labels))
> > > stop("Error: please specify the cell.types.labels!")
> > > if (nrow(ref.dat) != length(cell.type.labels))
> > > stop("Error: nrow(ref.dat) and length(cell.type.labels) need to be
the
> > > same!")
> > > if (is.null(n.cores.2g))
> > > n.cores.2g <- n.cores
> > > if (is.null(cell.subtype.labels))
> > > cell.subtype.labels <- cell.type.labels
> > > cell.type.labels <- as.character(cell.type.labels)
> > > cell.subtype.labels <- as.character(cell.subtype.labels)
> > > type.to.subtype.mapping <- unique(cbind(cell.type = cell.type.labels,
> > > cell.subtype = cell.subtype.labels))
> > > if (max(table(type.to.subtype.mapping[, "cell.subtype"])) >
> > > 1)
> > > stop("Error: one or more subtypes belong to multiple cell types!")
> > > if (length(unique(cell.type.labels)) >
> > > length(unique(cell.subtype.labels)))
> > > stop("Error: more cell types than subtypes!")
> > > print("removing non-numeric genes...")
> > > ref.dat <- ref.dat[, apply(ref.dat, 2, function(ref.dat.gene.i)
> > > as.logical(prod(is.numeric(ref.dat.gene.i),
> > > is.finite(ref.dat.gene.i))))]
> > > X <- X[, apply(X, 2, function(X.gene.i)
> > > as.logical(prod(is.numeric(X.gene.i),
> > > is.finite(X.gene.i)))), drop = F]
> > > print("removing outlier genes...")
> > > X.norm <- apply(X, 1, function(vec) vec/sum(vec))
> > > filter.idx <- apply(X.norm > outlier.cut, 1, sum)/ncol(X.norm) >
> > > outlier.fraction
> > > X <- X[, !filter.idx, drop = F]
> > > cat("Number of outlier genes filtered=", sum(filter.idx),
> > > "\n")
> > > if (!input.type %in% c("scRNA", "GEP"))
> > > stop("Error: please specify the correct input.type!")
> > > print("aligning reference and mixture...")
> > > if (input.type == "GEP") {
> > > stopifnot(nrow(ref.dat) == length(cell.type.labels))
> > > processed.dat <- process_GEP(ref = ref.dat, mixture = X,
> > > pseudo.min = pseudo.min, cell.type.labels = cell.type.labels)
> > > }
> > > if (input.type == "scRNA") {
> > > stopifnot(nrow(ref.dat) == length(cell.subtype.labels))
> > > processed.dat <- process_scRNA(ref = ref.dat, mixture = X,
> > > pseudo.min = pseudo.min, cell.type.labels = cell.type.labels,
> > > cell.subtype.labels = cell.subtype.labels)
> > > }
> > > if (!is.null(tum.key)) {
> > > tum.idx <- which(rownames(processed.dat$prior.matched.norm) ==
> > > tum.key)
> > > if (length(tum.idx) == 0)
> > > stop("Error: tum.key is not matched to any rownames of the reference,
> > > please check the spelling!")
> > > processed.dat$prior.matched.norm <-
> > > processed.dat$prior.matched.norm[-tum.idx,
> > > ]
> > > }
> > > else print("No tumor reference is speficied. Reference profiles are
> > > treated equally.")
> > > type.to.subtype.mapping <-
> > >
type.to.subtype.mapping[match(rownames(processed.dat$ref.matched.norm),
> > > type.to.subtype.mapping[, "cell.subtype"]), ]
> > > rm(ref.dat, X, cell.type.labels, cell.subtype.labels)
> > > gc()
> > > ted.res <- run.Ted.main(input.phi = processed.dat$ref.matched.norm,
> > > input.phi.prior = processed.dat$prior.matched.norm, X =
> > > processed.dat$mixture.matched,
> > > tum.key = tum.key, type.to.subtype.mapping = type.to.subtype.mapping,
> > > alpha = alpha, sigma = sigma, gibbs.control = gibbs.control,
> > > opt.control = opt.control, n.cores = n.cores, n.cores.2g =
n.cores.2g,
> > > first.gibbs.only = first.gibbs.only)
> > > para <- list(X = processed.dat$mixture.matched, input.phi =
> > > processed.dat$ref.matched.norm,
> > > input.phi.prior = processed.dat$prior.matched.norm, tum.key =
tum.key,
> > > type.to.subtype.mapping = type.to.subtype.mapping, alpha = alpha,
> > > sigma = sigma, pseudo.min = pseudo.min, gibbs.control =
gibbs.control,
> > > opt.control = opt.control, n.cores = n.cores)
> > > ted.res$para <- para
> > > if (!is.null(tum.key)) {
> > > Zkg.tum <- ted.res$res$first.gibbs.res$Zkg.tum
> > > Zkg.tum.round <- t(round(Zkg.tum))
> > > if.vst <- sum(apply(Zkg.tum.round, 1, min) == 0) <
nrow(Zkg.tum.round)
> > > if (if.vst & nrow(Zkg.tum.round) > 1) {
> > > print("vst transformation is feasible")
> > > Zkg.tum.vst <- vst(Zkg.tum.round, nsub = min(nrow(Zkg.tum.round)/5,
> > > 1000))
> > > cor.mat <- get.cormat(Zkg.tum = Zkg.tum.vst)
> > > }
> > > else {
> > > if (nrow(Zkg.tum.round) == 1)
> > > print("only one mixture sample. vst transformation is NOT feasible")
> > > else print("every gene has at least one zero. vst transformation is
NOT
> > > feasible")
> > > Zkg.tum.vst <- NULL
> > > cor.mat <- get.cormat(Zkg.tum =
> ted.res$res$first.gibbs.res$Zkg.tum.norm)
> > > }
> > > ted.res$res$first.gibbs.res$Zkg.tum.vst <- Zkg.tum.vst
> > > ted.res$res$first.gibbs.res$cor.mat <- cor.mat
> > > if (!is.null(pdf.name) & nrow(Zkg.tum.round) > 1)
> > > plot.heatmap(dat = cor.mat, pdf.name = pdf.name,
> > > cluster = T, self = T, show.value = F, metric = "is.cor")
> > > }
> > > return(ted.res)
> > > }
> > > <bytecode: 0x7f3c01e965c8>
> > > <environment: namespace:TED>
> > >
> > >
> > >
> > >
> > > > On 19 Jan 2022, at 20:56, Tinyi Chu ***@***.***> wrote:
> > > >
> > > >
> > > > Hi Huda,
> > > >
> > > > Yes. I think you did not update the package correctly. To check,
you
> > can
> > > > simply type run.Ted in your R console, and see if the argument
if.vst
> > is
> > > in
> > > > it.
> > > >
> > > > Best,
> > > >
> > > > Tinyi
> > > >
> > > >
> > > >
> > > > On Wed, Jan 19, 2022 at 3:54 PM Moh Huda ***@***.***> wrote:
> > > >
> > > > > Dear Tinyi,
> > > > >
> > > > > I have updated the package TED in R and have added the argument
> > if.vst
> > > =
> > > > > FALSE in runTED.R function This is to be precise what I have used
> > > > > run.Ted(ref.dat = filter_gene_scRNA_data, X = chosen_data,
> > > cell.type.labels
> > > > > = ***@***.***$seurat_clusters, cell.subtype.labels =
> > > > > ***@***.***$seurat_clusters, tum.key = "1", input.type = "scRNA",
> > > n.cores =
> > > > > 20, pdf.name = "tcga.tumor.synthetic", if.vst=FALSE). However, I
> got
> > > this
> > > > > error Error in run.Ted(ref.dat = filter_gene_scRNA_data, X =
> > > chosen_data,
> > > > > cell.type.labels = ***@***.***$seurat_clusters, :
> > > > > unused argument (if.vst = FALSE).
> > > > > 1. I suppose I use the argument incorrectly. a) Then where should
> > this
> > > > > argument be added then? b) Or is it possible that I might fail in
> > > updating
> > > > > the package which leads to this error message?
> > > > >
> > > > > 2. The version of the package TED I got is packageVersion("TED”)
> [1]
> > > > > ‘1.1’. Is it the correct one for the most updated?
> > > > >
> > > > >
> > > > > Thank you very much.
> > > > >
> > > > > Regards,
> > > > >
> > > > > Huda
> > > > > > On 17 Jan 2022, at 18:36, Tinyi Chu ***@***.***> wrote:
> > > > > >
> > > > > >
> > > > > > *Could you please direct me to the updated version if
possible?*
> > > > > > The github repository was updated yesterday. You may simply
> follow
> > > the
> > > > > > instructions on https://github.com/Danko-Lab/TED to install
> > > (upgrade).
> > > > > >
> > > > > >
> > > > > > *When you said "put if.vst=FALSE in the function argument", you
> > mean
> > > > > > thefunction run.Ted(..., if.vst=FALSE)?*
> > > > > > yes
> > > > > >
> > > > > > On Mon, Jan 17, 2022 at 1:31 PM Moh Huda ***@***.***> wrote:
> > > > > >
> > > > > > > Dear Tinyi,
> > > > > > >
> > > > > > > I am currently using the RStudio server and the last time I
> > > installed
> > > > > > > BayesPrism it was quite difficult and I need the admin help
to
> > > resolve
> > > > > the
> > > > > > > issue.
> > > > > > >
> > > > > > > Could you please direct me to the updated version if
possible?
> > > > > > >
> > > > > > > When you said "put if.vst=FALSE in the function argument",
you
> > > mean the
> > > > > > > function run.Ted(..., if.vst=FALSE)?
> > > > > > >
> > > > > > > I am sorry I am really bad at programming. Thank you for your
> > help
> > > and
> > > > > > > patience.
> > > > > > >
> > > > > > > Regards,
> > > > > > >
> > > > > > > Huda
> > > > > > >
> > > > > > > On Mon, 17 Jan 2022, 18:21 Tinyi Chu, ***@***.***> wrote:
> > > > > > >
> > > > > > > > Hi Huda,
> > > > > > > >
> > > > > > > > No, you do not need to change the code. You only need to
> > > re-install
> > > > > the
> > > > > > > > updated package, and put if.vst=FALSE in the function
> argument.
> > > > > > > >
> > > > > > > > Best,
> > > > > > > >
> > > > > > > > Tinyi
> > > > > > > >
> > > > > > > > On Mon, Jan 17, 2022 at 8:00 AM Moh Huda ***@***.***>
wrote:
> > > > > > > >
> > > > > > > > > Dear Tinyi,
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > I want to confirm that the line I need to modify is line
> 335
> > > from
> > > > > > > > > if(if.vst){
> > > > > > > > > becoming if(if.vst=FALSE){
> > > > > > > > >
> > > > > > > > > Is that all? Thank you very much for your help and reply.
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > Best regards,
> > > > > > > > >
> > > > > > > > > Huda
> > > > > > > > >
> > > > > > > > > On Mon, 17 Jan 2022, 07:40 Tinyi Chu, ***@***.***> wrote:
> > > > > > > > >
> > > > > > > > > > Hi Moh,
> > > > > > > > > >
> > > > > > > > > > Thank you for your question. This seems to be caused by
> the
> > > > > sparsity
> > > > > > > of
> > > > > > > > > > your simulated data. If you run vst (from the DEseq2
> > > package) on
> > > > > your
> > > > > > > > > > dataset, it gives the same error, which means that
there
> > are
> > > less
> > > > > > > than
> > > > > > > > > > 'nsub'(nsub=1000) rows with mean normalized count > 5.
> > > > > > > > > >
> > > > > > > > > > I added an argument of if.vst in the run.Ted function,
to
> > > allow
> > > > > you
> > > > > > > to
> > > > > > > > > > bypass the vst step. Simply set if.vst=FALSE, to
disable
> > vst.
> > > > > > > > > >
> > > > > > > > > > Let me know if there are any questions.
> > > > > > > > > >
> > > > > > > > > > Best,
> > > > > > > > > >
> > > > > > > > > > Tinyi
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > > On Sat, Jan 15, 2022 at 7:30 PM Moh Huda ***@***.***>
> > wrote:
> > > > > > > > > >
> > > > > > > > > > > I have some different types of data (real data,
> > > semisynthetic
> > > > > data,
> > > > > > > > and
> > > > > > > > > > > fully synthetic data generated using splatter
> software).
> > > When
> > > > > > > running
> > > > > > > > > the
> > > > > > > > > > > data and got the message "every gene has at least one
> > > zero. vst
> > > > > > > > > > > transformation is NOT feasible”, the running process
is
> > > > > successful.
> > > > > > > > > > > However, when running different data and got the
> message
> > > "vst
> > > > > > > > > > > transformation is feasible" the execution failed
> (running
> > > > > process
> > > > > > > > > > failed).
> > > > > > > > > > > The error message is
> > > > > > > > > > >
> > > > > > > > > > > 1. "Error in vst(Zkg.tum.round, nsub =
> > > > > min(nrow(Zkg.tum.round)/5,
> > > > > > > > > > > 1000)) :
> > > > > > > > > > > less than 'nsub' rows with mean normalized count > 5,
> > > > > > > > > > > it is recommended to use
> > varianceStabilizingTransformation
> > > > > > > directly".
> > > > > > > > > > >
> > > > > > > > > > > I check the file called runTed.R and this command is
in
> > > line
> > > > > 335.
> > > > > > > The
> > > > > > > > > > > suggestion there said that,
> > > > > > > > > > >
> > > > > > > > > > > 1. #adjust nsub, to avoid error when too few genes
are
> > used
> > > > > > > > > > > What I understand that I need to change the function
> > vst()
> > > on
> > > > > the
> > > > > > > > line
> > > > > > > > > > > 335 to varianceStabilizingTransformation(), but it
does
> > not
> > > > > work
> > > > > > > > > either.
> > > > > > > > > > > Also, I have no idea how to adjust nsub (the
suggestion
> > > number
> > > > > 2
> > > > > > > > > above).
> > > > > > > > > > >
> > > > > > > > > > > Could you please give a suggestion? Thank you.
> > > > > > > > > > >
> > > > > > > > > > > I attach the two sample data types.
> > > > > > > > > > > rstudio-export-2.zip
> > > > > > > > > > > <
> > > > > > >
> > > https://github.com/Danko-Lab/TED/files/7876152/rstudio-export-2.zip
> > > > > > > > >
> > > > > > > > > > >
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Dear Tinyi,
Finally, now I manage to make the function updated. I can see the function
for runTed.R is updated now (compared to the old one) and I'm sure it
indicates the installation was successful. It's quite tricky, but now all
is sorted. Thank you very much for your help and support.
Best regards,
Huda
…On Thu, 20 Jan 2022, 20:09 Tinyi Chu, ***@***.***> wrote:
please do a uninstall and re-install.
On Thu, Jan 20, 2022 at 3:01 PM Moh Huda ***@***.***> wrote:
> Dear Tinyi,
>
> I got the update from the admin. The message is
>
> "I tired installing again from github, and this time there was no error
> message saying that the github version was the same as that already
> installed. I guess an old version was cached somewhere, but you now have
> the latest release so hopefully this will work."
>
> Although the admin said it is successful, when I checked the runTed.R
> function, it still has the old function behaviour (without if.vst =
> FALSE). I had load the package using library(TED), then run the function
> runTed.R and as expected it was error saying "unused argument (if.vst =
> False).
>
> The version I got package.version("TED") is 1.1. Could you please advise
> what might be the problem?
>
> Thank you very much for your help.
>
> Best regards,
>
>
> Huda
>
> On Thu, 20 Jan 2022, 15:32 Tinyi Chu, ***@***.***> wrote:
>
> > The installation passed tests on my side. Please simply follow standard
> > uninstall and installation procedures. In case it still fails, please
> > forward me the exact error information. Thanks.
> >
> > On Thu, Jan 20, 2022 at 5:08 AM Moh Huda ***@***.***> wrote:
> >
> > > Dear Tinyi,
> > >
> > > I got this email from the admin for the server where I'm using the
> > RStudio
> > > for programming.
> > >
> > >
> > > "Dear Huda
> > >
> > >
> > >
> > > I re-installed the package, but it still said that the installed
> version
> > > is the same as the github version. It refuses to uninstall though.
Can
> > you
> > > get more details from the author of how to install and uninstall?
> > >
> > >
> > >
> > > As for the crashing problem, I think restarting r-server should fix
> this.
> > > I’ll need to warn those using it first.".
> > >
> > >
> > > I experienced the R crashing last night after the admin trying to
> update.
> > > He suspected there is something wrong when the update was run. Could
> you
> > > please advise us how to uninstall and reinstall the package correctly
> and
> > > safely?
> > >
> > >
> > > I really appreciate your help and understanding.
> > >
> > >
> > >
> > > Best regards,
> > >
> > >
> > > Huda
> > >
> > >
> > >
> > > Get Outlook for Android<https://aka.ms/AAb9ysg>
> > > ________________________________
> > > From: Tinyi Chu ***@***.***>
> > > Sent: Wednesday, January 19, 2022 9:58:31 PM
> > > To: Danko-Lab/TED ***@***.***>
> > > Cc: Moh Huda ***@***.***>; Author ***@***.***>
> > > Subject: Re: [Danko-Lab/TED] vst transformation is feasible, but
failed
> > > executing the next command (Issue #15)
> > >
> > >
> > > BayesPrism is not on CRAN yet. I did not update the version for this
> > > update. You may simply uninstall and re-install the latest github
> > > repository.
> > >
> > > On Wed, Jan 19, 2022 at 4:04 PM Moh Huda ***@***.***> wrote:
> > >
> > > > Dear Tinyi,
> > > >
> > > > Yes indeed, the argument is not in runTED yet. If successful, the
> > > argument
> > > > if.vst should be there, then. However, what is the TED package
> version
> > > for
> > > > the most updated one so that we can check if the most updated one
is
> > the
> > > > one that is installed? I tried to find this information on your
> Github
> > > > account or in the CRAN list but unfortunately I could not find it.
> > > >
> > > > Thank you very much.
> > > >
> > > > Regards,
> > > >
> > > > Huda
> > > >
> > > > > run.Ted
> > > > function (ref.dat, X, cell.type.labels, cell.subtype.labels = NULL,
> > > > tum.key = NULL, input.type, pseudo.min = 1e-08, alpha = 1,
> > > > sigma = 2, outlier.cut = 0.01, outlier.fraction = 0.1,
gibbs.control
> =
> > > > list(chain.length = 1000,
> > > > burn.in = 500, thinning = 2), opt.control = list(trace = 0,
> > > > maxit = 10000), n.cores = 1, n.cores.2g = NULL, pdf.name = NULL,
> > > > first.gibbs.only = F)
> > > > {
> > > > if (is.null(colnames(ref.dat)))
> > > > stop("Error: please specify the gene names of ref.dat!")
> > > > if (is.null(colnames(X)))
> > > > stop("Error: please specify the gene names of X!")
> > > > if (is.null(cell.type.labels))
> > > > stop("Error: please specify the cell.types.labels!")
> > > > if (nrow(ref.dat) != length(cell.type.labels))
> > > > stop("Error: nrow(ref.dat) and length(cell.type.labels) need to be
> the
> > > > same!")
> > > > if (is.null(n.cores.2g))
> > > > n.cores.2g <- n.cores
> > > > if (is.null(cell.subtype.labels))
> > > > cell.subtype.labels <- cell.type.labels
> > > > cell.type.labels <- as.character(cell.type.labels)
> > > > cell.subtype.labels <- as.character(cell.subtype.labels)
> > > > type.to.subtype.mapping <- unique(cbind(cell.type =
cell.type.labels,
> > > > cell.subtype = cell.subtype.labels))
> > > > if (max(table(type.to.subtype.mapping[, "cell.subtype"])) >
> > > > 1)
> > > > stop("Error: one or more subtypes belong to multiple cell types!")
> > > > if (length(unique(cell.type.labels)) >
> > > > length(unique(cell.subtype.labels)))
> > > > stop("Error: more cell types than subtypes!")
> > > > print("removing non-numeric genes...")
> > > > ref.dat <- ref.dat[, apply(ref.dat, 2, function(ref.dat.gene.i)
> > > > as.logical(prod(is.numeric(ref.dat.gene.i),
> > > > is.finite(ref.dat.gene.i))))]
> > > > X <- X[, apply(X, 2, function(X.gene.i)
> > > > as.logical(prod(is.numeric(X.gene.i),
> > > > is.finite(X.gene.i)))), drop = F]
> > > > print("removing outlier genes...")
> > > > X.norm <- apply(X, 1, function(vec) vec/sum(vec))
> > > > filter.idx <- apply(X.norm > outlier.cut, 1, sum)/ncol(X.norm) >
> > > > outlier.fraction
> > > > X <- X[, !filter.idx, drop = F]
> > > > cat("Number of outlier genes filtered=", sum(filter.idx),
> > > > "\n")
> > > > if (!input.type %in% c("scRNA", "GEP"))
> > > > stop("Error: please specify the correct input.type!")
> > > > print("aligning reference and mixture...")
> > > > if (input.type == "GEP") {
> > > > stopifnot(nrow(ref.dat) == length(cell.type.labels))
> > > > processed.dat <- process_GEP(ref = ref.dat, mixture = X,
> > > > pseudo.min = pseudo.min, cell.type.labels = cell.type.labels)
> > > > }
> > > > if (input.type == "scRNA") {
> > > > stopifnot(nrow(ref.dat) == length(cell.subtype.labels))
> > > > processed.dat <- process_scRNA(ref = ref.dat, mixture = X,
> > > > pseudo.min = pseudo.min, cell.type.labels = cell.type.labels,
> > > > cell.subtype.labels = cell.subtype.labels)
> > > > }
> > > > if (!is.null(tum.key)) {
> > > > tum.idx <- which(rownames(processed.dat$prior.matched.norm) ==
> > > > tum.key)
> > > > if (length(tum.idx) == 0)
> > > > stop("Error: tum.key is not matched to any rownames of the
reference,
> > > > please check the spelling!")
> > > > processed.dat$prior.matched.norm <-
> > > > processed.dat$prior.matched.norm[-tum.idx,
> > > > ]
> > > > }
> > > > else print("No tumor reference is speficied. Reference profiles are
> > > > treated equally.")
> > > > type.to.subtype.mapping <-
> > > >
> type.to.subtype.mapping[match(rownames(processed.dat$ref.matched.norm),
> > > > type.to.subtype.mapping[, "cell.subtype"]), ]
> > > > rm(ref.dat, X, cell.type.labels, cell.subtype.labels)
> > > > gc()
> > > > ted.res <- run.Ted.main(input.phi = processed.dat$ref.matched.norm,
> > > > input.phi.prior = processed.dat$prior.matched.norm, X =
> > > > processed.dat$mixture.matched,
> > > > tum.key = tum.key, type.to.subtype.mapping =
type.to.subtype.mapping,
> > > > alpha = alpha, sigma = sigma, gibbs.control = gibbs.control,
> > > > opt.control = opt.control, n.cores = n.cores, n.cores.2g =
> n.cores.2g,
> > > > first.gibbs.only = first.gibbs.only)
> > > > para <- list(X = processed.dat$mixture.matched, input.phi =
> > > > processed.dat$ref.matched.norm,
> > > > input.phi.prior = processed.dat$prior.matched.norm, tum.key =
> tum.key,
> > > > type.to.subtype.mapping = type.to.subtype.mapping, alpha = alpha,
> > > > sigma = sigma, pseudo.min = pseudo.min, gibbs.control =
> gibbs.control,
> > > > opt.control = opt.control, n.cores = n.cores)
> > > > ted.res$para <- para
> > > > if (!is.null(tum.key)) {
> > > > Zkg.tum <- ted.res$res$first.gibbs.res$Zkg.tum
> > > > Zkg.tum.round <- t(round(Zkg.tum))
> > > > if.vst <- sum(apply(Zkg.tum.round, 1, min) == 0) <
> nrow(Zkg.tum.round)
> > > > if (if.vst & nrow(Zkg.tum.round) > 1) {
> > > > print("vst transformation is feasible")
> > > > Zkg.tum.vst <- vst(Zkg.tum.round, nsub = min(nrow(Zkg.tum.round)/5,
> > > > 1000))
> > > > cor.mat <- get.cormat(Zkg.tum = Zkg.tum.vst)
> > > > }
> > > > else {
> > > > if (nrow(Zkg.tum.round) == 1)
> > > > print("only one mixture sample. vst transformation is NOT
feasible")
> > > > else print("every gene has at least one zero. vst transformation is
> NOT
> > > > feasible")
> > > > Zkg.tum.vst <- NULL
> > > > cor.mat <- get.cormat(Zkg.tum =
> > ted.res$res$first.gibbs.res$Zkg.tum.norm)
> > > > }
> > > > ted.res$res$first.gibbs.res$Zkg.tum.vst <- Zkg.tum.vst
> > > > ted.res$res$first.gibbs.res$cor.mat <- cor.mat
> > > > if (!is.null(pdf.name) & nrow(Zkg.tum.round) > 1)
> > > > plot.heatmap(dat = cor.mat, pdf.name = pdf.name,
> > > > cluster = T, self = T, show.value = F, metric = "is.cor")
> > > > }
> > > > return(ted.res)
> > > > }
> > > > <bytecode: 0x7f3c01e965c8>
> > > > <environment: namespace:TED>
> > > >
> > > >
> > > >
> > > >
> > > > > On 19 Jan 2022, at 20:56, Tinyi Chu ***@***.***> wrote:
> > > > >
> > > > >
> > > > > Hi Huda,
> > > > >
> > > > > Yes. I think you did not update the package correctly. To check,
> you
> > > can
> > > > > simply type run.Ted in your R console, and see if the argument
> if.vst
> > > is
> > > > in
> > > > > it.
> > > > >
> > > > > Best,
> > > > >
> > > > > Tinyi
> > > > >
> > > > >
> > > > >
> > > > > On Wed, Jan 19, 2022 at 3:54 PM Moh Huda ***@***.***> wrote:
> > > > >
> > > > > > Dear Tinyi,
> > > > > >
> > > > > > I have updated the package TED in R and have added the argument
> > > if.vst
> > > > =
> > > > > > FALSE in runTED.R function This is to be precise what I have
used
> > > > > > run.Ted(ref.dat = filter_gene_scRNA_data, X = chosen_data,
> > > > cell.type.labels
> > > > > > = ***@***.***$seurat_clusters, cell.subtype.labels =
> > > > > > ***@***.***$seurat_clusters, tum.key = "1", input.type =
"scRNA",
> > > > n.cores =
> > > > > > 20, pdf.name = "tcga.tumor.synthetic", if.vst=FALSE).
However, I
> > got
> > > > this
> > > > > > error Error in run.Ted(ref.dat = filter_gene_scRNA_data, X =
> > > > chosen_data,
> > > > > > cell.type.labels = ***@***.***$seurat_clusters, :
> > > > > > unused argument (if.vst = FALSE).
> > > > > > 1. I suppose I use the argument incorrectly. a) Then where
should
> > > this
> > > > > > argument be added then? b) Or is it possible that I might fail
in
> > > > updating
> > > > > > the package which leads to this error message?
> > > > > >
> > > > > > 2. The version of the package TED I got is
packageVersion("TED”)
> > [1]
> > > > > > ‘1.1’. Is it the correct one for the most updated?
> > > > > >
> > > > > >
> > > > > > Thank you very much.
> > > > > >
> > > > > > Regards,
> > > > > >
> > > > > > Huda
> > > > > > > On 17 Jan 2022, at 18:36, Tinyi Chu ***@***.***> wrote:
> > > > > > >
> > > > > > >
> > > > > > > *Could you please direct me to the updated version if
> possible?*
> > > > > > > The github repository was updated yesterday. You may simply
> > follow
> > > > the
> > > > > > > instructions on https://github.com/Danko-Lab/TED to install
> > > > (upgrade).
> > > > > > >
> > > > > > >
> > > > > > > *When you said "put if.vst=FALSE in the function argument",
you
> > > mean
> > > > > > > thefunction run.Ted(..., if.vst=FALSE)?*
> > > > > > > yes
> > > > > > >
> > > > > > > On Mon, Jan 17, 2022 at 1:31 PM Moh Huda ***@***.***> wrote:
> > > > > > >
> > > > > > > > Dear Tinyi,
> > > > > > > >
> > > > > > > > I am currently using the RStudio server and the last time I
> > > > installed
> > > > > > > > BayesPrism it was quite difficult and I need the admin help
> to
> > > > resolve
> > > > > > the
> > > > > > > > issue.
> > > > > > > >
> > > > > > > > Could you please direct me to the updated version if
> possible?
> > > > > > > >
> > > > > > > > When you said "put if.vst=FALSE in the function argument",
> you
> > > > mean the
> > > > > > > > function run.Ted(..., if.vst=FALSE)?
> > > > > > > >
> > > > > > > > I am sorry I am really bad at programming. Thank you for
your
> > > help
> > > > and
> > > > > > > > patience.
> > > > > > > >
> > > > > > > > Regards,
> > > > > > > >
> > > > > > > > Huda
> > > > > > > >
> > > > > > > > On Mon, 17 Jan 2022, 18:21 Tinyi Chu, ***@***.***> wrote:
> > > > > > > >
> > > > > > > > > Hi Huda,
> > > > > > > > >
> > > > > > > > > No, you do not need to change the code. You only need to
> > > > re-install
> > > > > > the
> > > > > > > > > updated package, and put if.vst=FALSE in the function
> > argument.
> > > > > > > > >
> > > > > > > > > Best,
> > > > > > > > >
> > > > > > > > > Tinyi
> > > > > > > > >
> > > > > > > > > On Mon, Jan 17, 2022 at 8:00 AM Moh Huda ***@***.***>
> wrote:
> > > > > > > > >
> > > > > > > > > > Dear Tinyi,
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > > I want to confirm that the line I need to modify is
line
> > 335
> > > > from
> > > > > > > > > > if(if.vst){
> > > > > > > > > > becoming if(if.vst=FALSE){
> > > > > > > > > >
> > > > > > > > > > Is that all? Thank you very much for your help and
reply.
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > > Best regards,
> > > > > > > > > >
> > > > > > > > > > Huda
> > > > > > > > > >
> > > > > > > > > > On Mon, 17 Jan 2022, 07:40 Tinyi Chu, ***@***.***>
wrote:
> > > > > > > > > >
> > > > > > > > > > > Hi Moh,
> > > > > > > > > > >
> > > > > > > > > > > Thank you for your question. This seems to be caused
by
> > the
> > > > > > sparsity
> > > > > > > > of
> > > > > > > > > > > your simulated data. If you run vst (from the DEseq2
> > > > package) on
> > > > > > your
> > > > > > > > > > > dataset, it gives the same error, which means that
> there
> > > are
> > > > less
> > > > > > > > than
> > > > > > > > > > > 'nsub'(nsub=1000) rows with mean normalized count >
5.
> > > > > > > > > > >
> > > > > > > > > > > I added an argument of if.vst in the run.Ted
function,
> to
> > > > allow
> > > > > > you
> > > > > > > > to
> > > > > > > > > > > bypass the vst step. Simply set if.vst=FALSE, to
> disable
> > > vst.
> > > > > > > > > > >
> > > > > > > > > > > Let me know if there are any questions.
> > > > > > > > > > >
> > > > > > > > > > > Best,
> > > > > > > > > > >
> > > > > > > > > > > Tinyi
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > > On Sat, Jan 15, 2022 at 7:30 PM Moh Huda ***@***.***>
> > > wrote:
> > > > > > > > > > >
> > > > > > > > > > > > I have some different types of data (real data,
> > > > semisynthetic
> > > > > > data,
> > > > > > > > > and
> > > > > > > > > > > > fully synthetic data generated using splatter
> > software).
> > > > When
> > > > > > > > running
> > > > > > > > > > the
> > > > > > > > > > > > data and got the message "every gene has at least
one
> > > > zero. vst
> > > > > > > > > > > > transformation is NOT feasible”, the running
process
> is
> > > > > > successful.
> > > > > > > > > > > > However, when running different data and got the
> > message
> > > > "vst
> > > > > > > > > > > > transformation is feasible" the execution failed
> > (running
> > > > > > process
> > > > > > > > > > > failed).
> > > > > > > > > > > > The error message is
> > > > > > > > > > > >
> > > > > > > > > > > > 1. "Error in vst(Zkg.tum.round, nsub =
> > > > > > min(nrow(Zkg.tum.round)/5,
> > > > > > > > > > > > 1000)) :
> > > > > > > > > > > > less than 'nsub' rows with mean normalized count >
5,
> > > > > > > > > > > > it is recommended to use
> > > varianceStabilizingTransformation
> > > > > > > > directly".
> > > > > > > > > > > >
> > > > > > > > > > > > I check the file called runTed.R and this command
is
> in
> > > > line
> > > > > > 335.
> > > > > > > > The
> > > > > > > > > > > > suggestion there said that,
> > > > > > > > > > > >
> > > > > > > > > > > > 1. #adjust nsub, to avoid error when too few genes
> are
> > > used
> > > > > > > > > > > > What I understand that I need to change the
function
> > > vst()
> > > > on
> > > > > > the
> > > > > > > > > line
> > > > > > > > > > > > 335 to varianceStabilizingTransformation(), but it
> does
> > > not
> > > > > > work
> > > > > > > > > > either.
> > > > > > > > > > > > Also, I have no idea how to adjust nsub (the
> suggestion
> > > > number
> > > > > > 2
> > > > > > > > > > above).
> > > > > > > > > > > >
> > > > > > > > > > > > Could you please give a suggestion? Thank you.
> > > > > > > > > > > >
> > > > > > > > > > > > I attach the two sample data types.
> > > > > > > > > > > > rstudio-export-2.zip
> > > > > > > > > > > > <
> > > > > > > >
> > > >
https://github.com/Danko-Lab/TED/files/7876152/rstudio-export-2.zip
> > > > > > > > > >
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You are welcome.
…On Thu, Jan 20, 2022 at 6:40 PM Moh Huda ***@***.***> wrote:
Dear Tinyi,
Finally, now I manage to make the function updated. I can see the function
for runTed.R is updated now (compared to the old one) and I'm sure it
indicates the installation was successful. It's quite tricky, but now all
is sorted. Thank you very much for your help and support.
Best regards,
Huda
On Thu, 20 Jan 2022, 20:09 Tinyi Chu, ***@***.***> wrote:
> please do a uninstall and re-install.
>
> On Thu, Jan 20, 2022 at 3:01 PM Moh Huda ***@***.***> wrote:
>
> > Dear Tinyi,
> >
> > I got the update from the admin. The message is
> >
> > "I tired installing again from github, and this time there was no error
> > message saying that the github version was the same as that already
> > installed. I guess an old version was cached somewhere, but you now
have
> > the latest release so hopefully this will work."
> >
> > Although the admin said it is successful, when I checked the runTed.R
> > function, it still has the old function behaviour (without if.vst =
> > FALSE). I had load the package using library(TED), then run the
function
> > runTed.R and as expected it was error saying "unused argument (if.vst =
> > False).
> >
> > The version I got package.version("TED") is 1.1. Could you please
advise
> > what might be the problem?
> >
> > Thank you very much for your help.
> >
> > Best regards,
> >
> >
> > Huda
> >
> > On Thu, 20 Jan 2022, 15:32 Tinyi Chu, ***@***.***> wrote:
> >
> > > The installation passed tests on my side. Please simply follow
standard
> > > uninstall and installation procedures. In case it still fails, please
> > > forward me the exact error information. Thanks.
> > >
> > > On Thu, Jan 20, 2022 at 5:08 AM Moh Huda ***@***.***> wrote:
> > >
> > > > Dear Tinyi,
> > > >
> > > > I got this email from the admin for the server where I'm using the
> > > RStudio
> > > > for programming.
> > > >
> > > >
> > > > "Dear Huda
> > > >
> > > >
> > > >
> > > > I re-installed the package, but it still said that the installed
> > version
> > > > is the same as the github version. It refuses to uninstall though.
> Can
> > > you
> > > > get more details from the author of how to install and uninstall?
> > > >
> > > >
> > > >
> > > > As for the crashing problem, I think restarting r-server should fix
> > this.
> > > > I’ll need to warn those using it first.".
> > > >
> > > >
> > > > I experienced the R crashing last night after the admin trying to
> > update.
> > > > He suspected there is something wrong when the update was run.
Could
> > you
> > > > please advise us how to uninstall and reinstall the package
correctly
> > and
> > > > safely?
> > > >
> > > >
> > > > I really appreciate your help and understanding.
> > > >
> > > >
> > > >
> > > > Best regards,
> > > >
> > > >
> > > > Huda
> > > >
> > > >
> > > >
> > > > Get Outlook for Android<https://aka.ms/AAb9ysg>
> > > > ________________________________
> > > > From: Tinyi Chu ***@***.***>
> > > > Sent: Wednesday, January 19, 2022 9:58:31 PM
> > > > To: Danko-Lab/TED ***@***.***>
> > > > Cc: Moh Huda ***@***.***>; Author ***@***.***>
> > > > Subject: Re: [Danko-Lab/TED] vst transformation is feasible, but
> failed
> > > > executing the next command (Issue #15)
> > > >
> > > >
> > > > BayesPrism is not on CRAN yet. I did not update the version for
this
> > > > update. You may simply uninstall and re-install the latest github
> > > > repository.
> > > >
> > > > On Wed, Jan 19, 2022 at 4:04 PM Moh Huda ***@***.***> wrote:
> > > >
> > > > > Dear Tinyi,
> > > > >
> > > > > Yes indeed, the argument is not in runTED yet. If successful, the
> > > > argument
> > > > > if.vst should be there, then. However, what is the TED package
> > version
> > > > for
> > > > > the most updated one so that we can check if the most updated one
> is
> > > the
> > > > > one that is installed? I tried to find this information on your
> > Github
> > > > > account or in the CRAN list but unfortunately I could not find
it.
> > > > >
> > > > > Thank you very much.
> > > > >
> > > > > Regards,
> > > > >
> > > > > Huda
> > > > >
> > > > > > run.Ted
> > > > > function (ref.dat, X, cell.type.labels, cell.subtype.labels =
NULL,
> > > > > tum.key = NULL, input.type, pseudo.min = 1e-08, alpha = 1,
> > > > > sigma = 2, outlier.cut = 0.01, outlier.fraction = 0.1,
> gibbs.control
> > =
> > > > > list(chain.length = 1000,
> > > > > burn.in = 500, thinning = 2), opt.control = list(trace = 0,
> > > > > maxit = 10000), n.cores = 1, n.cores.2g = NULL, pdf.name = NULL,
> > > > > first.gibbs.only = F)
> > > > > {
> > > > > if (is.null(colnames(ref.dat)))
> > > > > stop("Error: please specify the gene names of ref.dat!")
> > > > > if (is.null(colnames(X)))
> > > > > stop("Error: please specify the gene names of X!")
> > > > > if (is.null(cell.type.labels))
> > > > > stop("Error: please specify the cell.types.labels!")
> > > > > if (nrow(ref.dat) != length(cell.type.labels))
> > > > > stop("Error: nrow(ref.dat) and length(cell.type.labels) need to
be
> > the
> > > > > same!")
> > > > > if (is.null(n.cores.2g))
> > > > > n.cores.2g <- n.cores
> > > > > if (is.null(cell.subtype.labels))
> > > > > cell.subtype.labels <- cell.type.labels
> > > > > cell.type.labels <- as.character(cell.type.labels)
> > > > > cell.subtype.labels <- as.character(cell.subtype.labels)
> > > > > type.to.subtype.mapping <- unique(cbind(cell.type =
> cell.type.labels,
> > > > > cell.subtype = cell.subtype.labels))
> > > > > if (max(table(type.to.subtype.mapping[, "cell.subtype"])) >
> > > > > 1)
> > > > > stop("Error: one or more subtypes belong to multiple cell
types!")
> > > > > if (length(unique(cell.type.labels)) >
> > > > > length(unique(cell.subtype.labels)))
> > > > > stop("Error: more cell types than subtypes!")
> > > > > print("removing non-numeric genes...")
> > > > > ref.dat <- ref.dat[, apply(ref.dat, 2, function(ref.dat.gene.i)
> > > > > as.logical(prod(is.numeric(ref.dat.gene.i),
> > > > > is.finite(ref.dat.gene.i))))]
> > > > > X <- X[, apply(X, 2, function(X.gene.i)
> > > > > as.logical(prod(is.numeric(X.gene.i),
> > > > > is.finite(X.gene.i)))), drop = F]
> > > > > print("removing outlier genes...")
> > > > > X.norm <- apply(X, 1, function(vec) vec/sum(vec))
> > > > > filter.idx <- apply(X.norm > outlier.cut, 1, sum)/ncol(X.norm) >
> > > > > outlier.fraction
> > > > > X <- X[, !filter.idx, drop = F]
> > > > > cat("Number of outlier genes filtered=", sum(filter.idx),
> > > > > "\n")
> > > > > if (!input.type %in% c("scRNA", "GEP"))
> > > > > stop("Error: please specify the correct input.type!")
> > > > > print("aligning reference and mixture...")
> > > > > if (input.type == "GEP") {
> > > > > stopifnot(nrow(ref.dat) == length(cell.type.labels))
> > > > > processed.dat <- process_GEP(ref = ref.dat, mixture = X,
> > > > > pseudo.min = pseudo.min, cell.type.labels = cell.type.labels)
> > > > > }
> > > > > if (input.type == "scRNA") {
> > > > > stopifnot(nrow(ref.dat) == length(cell.subtype.labels))
> > > > > processed.dat <- process_scRNA(ref = ref.dat, mixture = X,
> > > > > pseudo.min = pseudo.min, cell.type.labels = cell.type.labels,
> > > > > cell.subtype.labels = cell.subtype.labels)
> > > > > }
> > > > > if (!is.null(tum.key)) {
> > > > > tum.idx <- which(rownames(processed.dat$prior.matched.norm) ==
> > > > > tum.key)
> > > > > if (length(tum.idx) == 0)
> > > > > stop("Error: tum.key is not matched to any rownames of the
> reference,
> > > > > please check the spelling!")
> > > > > processed.dat$prior.matched.norm <-
> > > > > processed.dat$prior.matched.norm[-tum.idx,
> > > > > ]
> > > > > }
> > > > > else print("No tumor reference is speficied. Reference profiles
are
> > > > > treated equally.")
> > > > > type.to.subtype.mapping <-
> > > > >
> > type.to.subtype.mapping[match(rownames(processed.dat$ref.matched.norm),
> > > > > type.to.subtype.mapping[, "cell.subtype"]), ]
> > > > > rm(ref.dat, X, cell.type.labels, cell.subtype.labels)
> > > > > gc()
> > > > > ted.res <- run.Ted.main(input.phi =
processed.dat$ref.matched.norm,
> > > > > input.phi.prior = processed.dat$prior.matched.norm, X =
> > > > > processed.dat$mixture.matched,
> > > > > tum.key = tum.key, type.to.subtype.mapping =
> type.to.subtype.mapping,
> > > > > alpha = alpha, sigma = sigma, gibbs.control = gibbs.control,
> > > > > opt.control = opt.control, n.cores = n.cores, n.cores.2g =
> > n.cores.2g,
> > > > > first.gibbs.only = first.gibbs.only)
> > > > > para <- list(X = processed.dat$mixture.matched, input.phi =
> > > > > processed.dat$ref.matched.norm,
> > > > > input.phi.prior = processed.dat$prior.matched.norm, tum.key =
> > tum.key,
> > > > > type.to.subtype.mapping = type.to.subtype.mapping, alpha = alpha,
> > > > > sigma = sigma, pseudo.min = pseudo.min, gibbs.control =
> > gibbs.control,
> > > > > opt.control = opt.control, n.cores = n.cores)
> > > > > ted.res$para <- para
> > > > > if (!is.null(tum.key)) {
> > > > > Zkg.tum <- ted.res$res$first.gibbs.res$Zkg.tum
> > > > > Zkg.tum.round <- t(round(Zkg.tum))
> > > > > if.vst <- sum(apply(Zkg.tum.round, 1, min) == 0) <
> > nrow(Zkg.tum.round)
> > > > > if (if.vst & nrow(Zkg.tum.round) > 1) {
> > > > > print("vst transformation is feasible")
> > > > > Zkg.tum.vst <- vst(Zkg.tum.round, nsub =
min(nrow(Zkg.tum.round)/5,
> > > > > 1000))
> > > > > cor.mat <- get.cormat(Zkg.tum = Zkg.tum.vst)
> > > > > }
> > > > > else {
> > > > > if (nrow(Zkg.tum.round) == 1)
> > > > > print("only one mixture sample. vst transformation is NOT
> feasible")
> > > > > else print("every gene has at least one zero. vst transformation
is
> > NOT
> > > > > feasible")
> > > > > Zkg.tum.vst <- NULL
> > > > > cor.mat <- get.cormat(Zkg.tum =
> > > ted.res$res$first.gibbs.res$Zkg.tum.norm)
> > > > > }
> > > > > ted.res$res$first.gibbs.res$Zkg.tum.vst <- Zkg.tum.vst
> > > > > ted.res$res$first.gibbs.res$cor.mat <- cor.mat
> > > > > if (!is.null(pdf.name) & nrow(Zkg.tum.round) > 1)
> > > > > plot.heatmap(dat = cor.mat, pdf.name = pdf.name,
> > > > > cluster = T, self = T, show.value = F, metric = "is.cor")
> > > > > }
> > > > > return(ted.res)
> > > > > }
> > > > > <bytecode: 0x7f3c01e965c8>
> > > > > <environment: namespace:TED>
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > > On 19 Jan 2022, at 20:56, Tinyi Chu ***@***.***> wrote:
> > > > > >
> > > > > >
> > > > > > Hi Huda,
> > > > > >
> > > > > > Yes. I think you did not update the package correctly. To
check,
> > you
> > > > can
> > > > > > simply type run.Ted in your R console, and see if the argument
> > if.vst
> > > > is
> > > > > in
> > > > > > it.
> > > > > >
> > > > > > Best,
> > > > > >
> > > > > > Tinyi
> > > > > >
> > > > > >
> > > > > >
> > > > > > On Wed, Jan 19, 2022 at 3:54 PM Moh Huda ***@***.***> wrote:
> > > > > >
> > > > > > > Dear Tinyi,
> > > > > > >
> > > > > > > I have updated the package TED in R and have added the
argument
> > > > if.vst
> > > > > =
> > > > > > > FALSE in runTED.R function This is to be precise what I have
> used
> > > > > > > run.Ted(ref.dat = filter_gene_scRNA_data, X = chosen_data,
> > > > > cell.type.labels
> > > > > > > = ***@***.***$seurat_clusters, cell.subtype.labels =
> > > > > > > ***@***.***$seurat_clusters, tum.key = "1", input.type =
> "scRNA",
> > > > > n.cores =
> > > > > > > 20, pdf.name = "tcga.tumor.synthetic", if.vst=FALSE).
> However, I
> > > got
> > > > > this
> > > > > > > error Error in run.Ted(ref.dat = filter_gene_scRNA_data, X =
> > > > > chosen_data,
> > > > > > > cell.type.labels = ***@***.***$seurat_clusters, :
> > > > > > > unused argument (if.vst = FALSE).
> > > > > > > 1. I suppose I use the argument incorrectly. a) Then where
> should
> > > > this
> > > > > > > argument be added then? b) Or is it possible that I might
fail
> in
> > > > > updating
> > > > > > > the package which leads to this error message?
> > > > > > >
> > > > > > > 2. The version of the package TED I got is
> packageVersion("TED”)
> > > [1]
> > > > > > > ‘1.1’. Is it the correct one for the most updated?
> > > > > > >
> > > > > > >
> > > > > > > Thank you very much.
> > > > > > >
> > > > > > > Regards,
> > > > > > >
> > > > > > > Huda
> > > > > > > > On 17 Jan 2022, at 18:36, Tinyi Chu ***@***.***> wrote:
> > > > > > > >
> > > > > > > >
> > > > > > > > *Could you please direct me to the updated version if
> > possible?*
> > > > > > > > The github repository was updated yesterday. You may simply
> > > follow
> > > > > the
> > > > > > > > instructions on https://github.com/Danko-Lab/TED to
install
> > > > > (upgrade).
> > > > > > > >
> > > > > > > >
> > > > > > > > *When you said "put if.vst=FALSE in the function argument",
> you
> > > > mean
> > > > > > > > thefunction run.Ted(..., if.vst=FALSE)?*
> > > > > > > > yes
> > > > > > > >
> > > > > > > > On Mon, Jan 17, 2022 at 1:31 PM Moh Huda ***@***.***>
wrote:
> > > > > > > >
> > > > > > > > > Dear Tinyi,
> > > > > > > > >
> > > > > > > > > I am currently using the RStudio server and the last
time I
> > > > > installed
> > > > > > > > > BayesPrism it was quite difficult and I need the admin
help
> > to
> > > > > resolve
> > > > > > > the
> > > > > > > > > issue.
> > > > > > > > >
> > > > > > > > > Could you please direct me to the updated version if
> > possible?
> > > > > > > > >
> > > > > > > > > When you said "put if.vst=FALSE in the function
argument",
> > you
> > > > > mean the
> > > > > > > > > function run.Ted(..., if.vst=FALSE)?
> > > > > > > > >
> > > > > > > > > I am sorry I am really bad at programming. Thank you for
> your
> > > > help
> > > > > and
> > > > > > > > > patience.
> > > > > > > > >
> > > > > > > > > Regards,
> > > > > > > > >
> > > > > > > > > Huda
> > > > > > > > >
> > > > > > > > > On Mon, 17 Jan 2022, 18:21 Tinyi Chu, ***@***.***> wrote:
> > > > > > > > >
> > > > > > > > > > Hi Huda,
> > > > > > > > > >
> > > > > > > > > > No, you do not need to change the code. You only need
to
> > > > > re-install
> > > > > > > the
> > > > > > > > > > updated package, and put if.vst=FALSE in the function
> > > argument.
> > > > > > > > > >
> > > > > > > > > > Best,
> > > > > > > > > >
> > > > > > > > > > Tinyi
> > > > > > > > > >
> > > > > > > > > > On Mon, Jan 17, 2022 at 8:00 AM Moh Huda ***@***.***>
> > wrote:
> > > > > > > > > >
> > > > > > > > > > > Dear Tinyi,
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > > I want to confirm that the line I need to modify is
> line
> > > 335
> > > > > from
> > > > > > > > > > > if(if.vst){
> > > > > > > > > > > becoming if(if.vst=FALSE){
> > > > > > > > > > >
> > > > > > > > > > > Is that all? Thank you very much for your help and
> reply.
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > > Best regards,
> > > > > > > > > > >
> > > > > > > > > > > Huda
> > > > > > > > > > >
> > > > > > > > > > > On Mon, 17 Jan 2022, 07:40 Tinyi Chu, ***@***.***>
> wrote:
> > > > > > > > > > >
> > > > > > > > > > > > Hi Moh,
> > > > > > > > > > > >
> > > > > > > > > > > > Thank you for your question. This seems to be
caused
> by
> > > the
> > > > > > > sparsity
> > > > > > > > > of
> > > > > > > > > > > > your simulated data. If you run vst (from the
DEseq2
> > > > > package) on
> > > > > > > your
> > > > > > > > > > > > dataset, it gives the same error, which means that
> > there
> > > > are
> > > > > less
> > > > > > > > > than
> > > > > > > > > > > > 'nsub'(nsub=1000) rows with mean normalized count >
> 5.
> > > > > > > > > > > >
> > > > > > > > > > > > I added an argument of if.vst in the run.Ted
> function,
> > to
> > > > > allow
> > > > > > > you
> > > > > > > > > to
> > > > > > > > > > > > bypass the vst step. Simply set if.vst=FALSE, to
> > disable
> > > > vst.
> > > > > > > > > > > >
> > > > > > > > > > > > Let me know if there are any questions.
> > > > > > > > > > > >
> > > > > > > > > > > > Best,
> > > > > > > > > > > >
> > > > > > > > > > > > Tinyi
> > > > > > > > > > > >
> > > > > > > > > > > >
> > > > > > > > > > > > On Sat, Jan 15, 2022 at 7:30 PM Moh Huda
***@***.***>
> > > > wrote:
> > > > > > > > > > > >
> > > > > > > > > > > > > I have some different types of data (real data,
> > > > > semisynthetic
> > > > > > > data,
> > > > > > > > > > and
> > > > > > > > > > > > > fully synthetic data generated using splatter
> > > software).
> > > > > When
> > > > > > > > > running
> > > > > > > > > > > the
> > > > > > > > > > > > > data and got the message "every gene has at least
> one
> > > > > zero. vst
> > > > > > > > > > > > > transformation is NOT feasible”, the running
> process
> > is
> > > > > > > successful.
> > > > > > > > > > > > > However, when running different data and got the
> > > message
> > > > > "vst
> > > > > > > > > > > > > transformation is feasible" the execution failed
> > > (running
> > > > > > > process
> > > > > > > > > > > > failed).
> > > > > > > > > > > > > The error message is
> > > > > > > > > > > > >
> > > > > > > > > > > > > 1. "Error in vst(Zkg.tum.round, nsub =
> > > > > > > min(nrow(Zkg.tum.round)/5,
> > > > > > > > > > > > > 1000)) :
> > > > > > > > > > > > > less than 'nsub' rows with mean normalized count
>
> 5,
> > > > > > > > > > > > > it is recommended to use
> > > > varianceStabilizingTransformation
> > > > > > > > > directly".
> > > > > > > > > > > > >
> > > > > > > > > > > > > I check the file called runTed.R and this command
> is
> > in
> > > > > line
> > > > > > > 335.
> > > > > > > > > The
> > > > > > > > > > > > > suggestion there said that,
> > > > > > > > > > > > >
> > > > > > > > > > > > > 1. #adjust nsub, to avoid error when too few
genes
> > are
> > > > used
> > > > > > > > > > > > > What I understand that I need to change the
> function
> > > > vst()
> > > > > on
> > > > > > > the
> > > > > > > > > > line
> > > > > > > > > > > > > 335 to varianceStabilizingTransformation(), but
it
> > does
> > > > not
> > > > > > > work
> > > > > > > > > > > either.
> > > > > > > > > > > > > Also, I have no idea how to adjust nsub (the
> > suggestion
> > > > > number
> > > > > > > 2
> > > > > > > > > > > above).
> > > > > > > > > > > > >
> > > > > > > > > > > > > Could you please give a suggestion? Thank you.
> > > > > > > > > > > > >
> > > > > > > > > > > > > I attach the two sample data types.
> > > > > > > > > > > > > rstudio-export-2.zip
> > > > > > > > > > > > > <
> > > > > > > > >
> > > > >
> https://github.com/Danko-Lab/TED/files/7876152/rstudio-export-2.zip
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I have some different types of data (real data, semisynthetic data, and fully synthetic data generated using splatter software). When running the data and got the message "every gene has at least one zero. vst transformation is NOT feasible”, the running process is successful. However, when running different data and got the message "vst transformation is feasible" the execution failed (running process failed). The error message is
less than 'nsub' rows with mean normalized count > 5,
it is recommended to use varianceStabilizingTransformation directly".
I check the file called runTed.R and this command is in line 335. The suggestion there said that,
What I understand that I need to change the function vst() on the line 335 to varianceStabilizingTransformation(), but it does not work either. Also, I have no idea how to adjust nsub (the suggestion number 2 above).
Could you please give a suggestion? Thank you.
I attach the two sample data types.
rstudio-export-2.zip
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