Z expression matrix

[martina811]

Hello,
I would like to know what is the step in Bayes Prism where the Z matrix, that we found in posterior.initial.state/type, is generated?

Thanks a lot for your help

[tinyi]

Hi. I wasn’t quite sure I understand your question. Could you elaborate a bit?

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On Wed, Nov 29, 2023 at 19:10 biomart811 ***@***.***> wrote: Hello, I would like to know what is the step in Bayes Prism where the Z matrix, that we found in posterior.initial.state/type, is generated? Thanks a lot for your help — Reply to this email directly, view it on GitHub <#68>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB4NHSZJZZUM67HHUITVLE3YG4JZNAVCNFSM6AAAAAA77IYOKWVHI2DSMVQWIX3LMV43ASLTON2WKOZSGAYTMMZUHA4TONQ> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[martina811]

I am using Bayes Prism, and I want to use it as a tool for having a measure of confidence of my results. So I was wondering if I can extract the posterior probability on which bayes prism based its results in θf.

[tinyi]

Hi. BayesPrism reports the coefficient of variation for the posteriors theta0 and thetaf, but does not report this for Z, mainly due to consideration of computational and memory efficiency.

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On Wed, Dec 13, 2023 at 22:21 biomart811 ***@***.***> wrote: I am using Bayes Prism, and I want to use it as a tool for having a measure of confidence of my results. So I was wondering if I can extract the posterior probability on which bayes prism based its results in θf. — Reply to this email directly, view it on GitHub <#68 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB4NHS6BIOJEZ54MBMIK3L3YJG2WBAVCNFSM6AAAAAA77IYOKWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNJUGAYDOMJXGY> . You are receiving this because you commented.Message ID: ***@***.***>

[martina811]

And there is a way to calculate the posterior probability that bayes prism use for update thetaf starting from theta0 ?
Thank you

[tinyi]

Not sure if I understand the question. For the exact math, please refer to the BayesPrism manuscript. For the code, please refer to the update_reference.R .

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On Thu, Dec 14, 2023 at 5:36 PM biomart811 ***@***.***> wrote: And there is a way to calculate the posterior probability that bayes prism use for update thetaf starting from theta0 ? Thank you — Reply to this email directly, view it on GitHub <#68 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB4NHS32CI4D5V4HTAG6GKDYJLCBTAVCNFSM6AAAAAA77IYOKWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNJVGQ4TQMJYHE> . You are receiving this because you commented.Message ID: ***@***.***>

[martina811]

my question is if from Bayes Prism there is a way to obtain a measure of confidence for the updated thetaf that Bayes Prism provides.

[tinyi]

please refer to the vignette tutorial_deconvolution.html # extract coefficient of variation (CV) of cell type fractiontheta.cv <- ***@***.******@***.***

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On Thu, Dec 14, 2023 at 5:47 PM biomart811 ***@***.***> wrote: my question is if from Bayes Prism there is a way to obtain a measure of confidence for the updated thetaf that Bayes Prism provides. — Reply to this email directly, view it on GitHub <#68 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB4NHSY5EYB543E2BAD4ITLYJLDJNAVCNFSM6AAAAAA77IYOKWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNJVGUYTOMRTG4> . You are receiving this because you commented.Message ID: ***@***.***>