creating signature

[Laurent2873]

Hi,

I have created a named vector and I used 1 for the value of every gene.

str(sigData)
Named num [1:253] 1 1 1 1 1 1 1 1 1 1 ...

• attr(*, "names")= chr [1:253] "IFIT3" "IFIT3B" "IFIT1" "ISG15" ...

signature <- createGeneSignature(name = "Signature", sigData = sigData)

mySignature <- c(signature)

vision.obj <- Vision(filtered_seurat, signatures = mySignature, projection_methods = NULL)

vision.obj <- analyze(vision.obj)
Beginning Analysis

Clustering cells...completed

Projecting data into 2 dimensions...

Evaluating signature scores on cells...

|==============================================================================================| 100%, Elapsed 00:00
Evaluating signature-gene importance...

| | 0%, ETA NA
Error in E %% Cs %% S - Rog %% (Roc %% S) + Cog %% (Coc %% (Cs %*% :
Matrices must have same number of rows for arithmetic

I can run with signatures when loaded from MisigDb but I get this error when I load my signature. I must be doing something wrong in creating the signature from the file.
Any help appreciated.

Thanks

[mattjones315]

Thanks for posting this issue. It is difficult to diagnose this issue without seeing a block of code / data that can reproduce this error. Could you please provide this? Three things to check though - first, would you try passing a named list instead of a named vector? Second, are you sure the genes in your signature appear in your transcriptome? Last, does this problem persist if you run VISION with MSigDB signatures and this user-defined signature? Thanks, Matt

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On Tue, Nov 23, 2021 at 4:49 PM Laurent2873 ***@***.***> wrote: Hi, I have created a named vector and I used 1 for the value of every gene. str(sigData) Named num [1:253] 1 1 1 1 1 1 1 1 1 1 ... - attr(*, "names")= chr [1:253] "IFIT3" "IFIT3B" "IFIT1" "ISG15" ... signature <- createGeneSignature(name = "Signature", sigData = sigData) mySignature <- c(signature) vision.obj <- Vision(filtered_seurat, signatures = mySignature, projection_methods = NULL) vision.obj <- analyze(vision.obj) Beginning Analysis Clustering cells...completed Projecting data into 2 dimensions... Evaluating signature scores on cells... |==============================================================================================| 100%, Elapsed 00:00 Evaluating signature-gene importance... | | 0%, ETA NA Error in E %*% Cs %*% S - Rog %*% (Roc %*% S) + Cog %*% (Coc %*% (Cs %*% : Matrices must have same number of rows for arithmetic I can run with signatures when loaded from MisigDb but I get this error when I load my signature. I must be doing something wrong in creating the signature from the file. Any help appreciated. Thanks — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#101>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACKWFHVHDZVZVJPI6AULYHLUNQZAFANCNFSM5IU2BAKQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

[Laurent2873]

Thanks Matt for your prompt answer!! Much appreciated. I will be able to provide the code/data when I get back to lab. If I combine the MsigDB signature and my signature, it seems to run but ignores my signature (ie. No results from it but I do get GO enrichment from MsigDB). I tried that once but my vector might not have been named when I did that. I realized subsequently that it needed to be a named vector, which I now have. About the rest, I have thought a little bit about the various issues you raise and I don’t have a formal answer yet. I’m trying to make a signature from a mouse data set and then see whether I can see some “enrichment” for this signature with similar data but from human samples. I did capitalize the gene names but it is certainly possible that some do not match, although quite a few should. I was thinking of trying to clean up and use only gene names that would be common to both species. I haven’t tried that yet. I also need to try to pass the named vector directly. Thanks again for your help, Laurent

…

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On Nov 24, 2021, at 9:37 AM, Matt Jones ***@***.***> wrote:  Thanks for posting this issue. It is difficult to diagnose this issue without seeing a block of code / data that can reproduce this error. Could you please provide this? Three things to check though - first, would you try passing a named list instead of a named vector? Second, are you sure the genes in your signature appear in your transcriptome? Last, does this problem persist if you run VISION with MSigDB signatures and this user-defined signature? Thanks, Matt On Tue, Nov 23, 2021 at 4:49 PM Laurent2873 ***@***.***> wrote: > Hi, > > I have created a named vector and I used 1 for the value of every gene. > > str(sigData) > Named num [1:253] 1 1 1 1 1 1 1 1 1 1 ... > > - attr(*, "names")= chr [1:253] "IFIT3" "IFIT3B" "IFIT1" "ISG15" ... > > signature <- createGeneSignature(name = "Signature", sigData = sigData) > > mySignature <- c(signature) > > vision.obj <- Vision(filtered_seurat, signatures = mySignature, > projection_methods = NULL) > > vision.obj <- analyze(vision.obj) > Beginning Analysis > > Clustering cells...completed > > Projecting data into 2 dimensions... > > Evaluating signature scores on cells... > > |==============================================================================================| > 100%, Elapsed 00:00 > Evaluating signature-gene importance... > > | | 0%, ETA NA > Error in E %*% Cs %*% S - Rog %*% (Roc %*% S) + Cog %*% (Coc %*% (Cs %*% : > Matrices must have same number of rows for arithmetic > > I can run with signatures when loaded from MisigDb but I get this error > when I load my signature. I must be doing something wrong in creating the > signature from the file. > Any help appreciated. > > Thanks > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub > <#101>, or unsubscribe > <https://github.com/notifications/unsubscribe-auth/ACKWFHVHDZVZVJPI6AULYHLUNQZAFANCNFSM5IU2BAKQ> > . > Triage notifications on the go with GitHub Mobile for iOS > <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> > or Android > <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. > > — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android.

[Laurent2873]

Matt, I have resolved the issue. I had to intersect the genes in my signatures with the genes that are in the data. Since I was using Mouse genes for a signature to project to human data, some of the genes didn’t exist. It’s now working but I have a question regarding the interpretation if you don’t mind. For example, I ran several of my signatures and the Hallmark from MSigDB. I get these results. Can I conclude with a C’ value of 0.37 and 0.38 that I indeed gets some cells with a correlation of these signatures? What is a reasonable cut off for the C’ value (even if the FDR is <0.001). Thanks Laurent C pValue FDR HALLMARK_MYC_TARGETS_V1 0.4265816 0.0003332223 0.001116295 HALLMARK_INTERFERON_GAMMA_RESPONSE 0.3928432 0.0003332223 0.001116295 Stage0 Signature 0.3843447 0.0003332223 0.001116295 NKT1 Signature 0.3700731 0.0003332223 0.001116295 HALLMARK_INTERFERON_ALPHA_RESPONSE 0.3570704 0.0003332223 0.001116295 HALLMARK_ALLOGRAFT_REJECTION 0.2961219 0.0003332223 0.001116295

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On Nov 24, 2021, at 9:37 AM, Matt Jones ***@***.***> wrote: Thanks for posting this issue. It is difficult to diagnose this issue without seeing a block of code / data that can reproduce this error. Could you please provide this? Three things to check though - first, would you try passing a named list instead of a named vector? Second, are you sure the genes in your signature appear in your transcriptome? Last, does this problem persist if you run VISION with MSigDB signatures and this user-defined signature? Thanks, Matt On Tue, Nov 23, 2021 at 4:49 PM Laurent2873 ***@***.***> wrote: > Hi, > > I have created a named vector and I used 1 for the value of every gene. > > str(sigData) > Named num [1:253] 1 1 1 1 1 1 1 1 1 1 ... > > - attr(*, "names")= chr [1:253] "IFIT3" "IFIT3B" "IFIT1" "ISG15" ... > > signature <- createGeneSignature(name = "Signature", sigData = sigData) > > mySignature <- c(signature) > > vision.obj <- Vision(filtered_seurat, signatures = mySignature, > projection_methods = NULL) > > vision.obj <- analyze(vision.obj) > Beginning Analysis > > Clustering cells...completed > > Projecting data into 2 dimensions... > > Evaluating signature scores on cells... > > |==============================================================================================| > 100%, Elapsed 00:00 > Evaluating signature-gene importance... > > | | 0%, ETA NA > Error in E %*% Cs %*% S - Rog %*% (Roc %*% S) + Cog %*% (Coc %*% (Cs %*% : > Matrices must have same number of rows for arithmetic > > I can run with signatures when loaded from MisigDb but I get this error > when I load my signature. I must be doing something wrong in creating the > signature from the file. > Any help appreciated. > > Thanks > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub > <#101>, or unsubscribe > <https://github.com/notifications/unsubscribe-auth/ACKWFHVHDZVZVJPI6AULYHLUNQZAFANCNFSM5IU2BAKQ> > . > Triage notifications on the go with GitHub Mobile for iOS > <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> > or Android > <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. > > — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#101 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALZVGW6MOE4TOKJ3MHDDG23UNUIC3ANCNFSM5IU2BAKQ>. Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

[Laurent2873]

I resolved my issue by making sure that the genes in the signatures are indeed in the data.

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On Feb 17, 2022, at 11:43 AM, Ellen Ruth A. Morris ***@***.***> wrote: Hi - I am having a similar issue with trying to generate a signature score from a self generated gmt file. I have tried all the suggested resolutions and none have work. I have also reformatted my gmt file to be the same as a MSigDB gmt file. I also do not have this error output when I run the MSigDB gmt files alone. If you have any suggestions to resolve this issue, it would be greatly appreciated. Please see my code and output below: CODE: sig <- c("c2.cp.reactome.v7.5.1.symbols.gmt", "Cholesterol_GSEA.gmt") P27vP23_vision.obj2 <- Vision(P27vP23_sce, signatures = sig, meta = P27vP23_meta)Seurat object P27vP23_vision.obj2 <- analyze(P27vP23_vision.obj2) ERROR OUTPUT: P27vP23_vision.obj2 <- analyze(P27vP23_vision.obj2) # running the entire VISION analysis pipeline and populates VISION object with results Beginning Analysis Clustering cells...completed Projecting data into 2 dimensions... Running method 1/1: tSNE30 ... Evaluating signature scores on cells... |=========================================================================================================| 100%, Elapsed 00:03Evaluating signature-gene importance... |============================================================================================================ | 99%, ETA 00:01Error in E %% Cs %% S - Rog %% (Roc %% S) + Cog %% (Coc %% (Cs %*% : Matrices must have same number of rows for arithmetic — Reply to this email directly, view it on GitHub <#101 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALZVGW7NQ5HAARWRURAW2ZDU3U6WFANCNFSM5IU2BAKQ>. Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you authored the thread.