search

Danko-Lab / BayesPrism

A Fully Bayesian Inference of Tumor Microenvironment composition and gene expression
145 stars 45 forks source link

Can I used BayesPrism to perform deconvolution on the microarray results by the scRNAseq reference #96

Open ZhijieHanbioinfor opened 1 month ago

ZhijieHanbioinfor commented 1 month ago

Can I used BayesPrism to perform deconvolution on the microarray results (e.g., RMA expression values) by the scRNAseq reference? Suppose I take the relative expressions of RMA values and scRNAseq counts beforehand, respectively.

tinyi commented 3 weeks ago

Dear user,

Thank you for your interest in our methods.

We have not tested if microarray data can be used as reference. We noted one recent study that applied BayesPrism to deconovovle the microarray bulk (https://www.biorxiv.org/content/10.1101/2023.06.14.544991v1.full), which seems to perform well. You may give it a try and see if the results make sense.

You may also try using markers when constructing the scRNA-seq reference to overcome the strong technical difference between RNA-seq and microarray data to see if it improves the results (provided you have some prior knowledge about the ground truth).

Best,

Tinyi

tinyi commented 3 weeks ago

Hi Zhijie,

Thank you for your questions. Please refer to this reply: https://github.com/Danko-Lab/BayesPrism/issues/56#issuecomment-1669620258

Best,

Tinyi

On Mon, Aug 19, 2024 at 12:54 AM ZhijieHanbioinfor @.***> wrote:

Dear Dr. Chu,

Thank you for your reply. I have another question. I want to merge multiple single cell samples as reference, which requires removing the batch effect. After removing the batch effect there will no longer be the counts values, will this have an effect on the BayesPrism analysis? Or the BayesPrism analysis doesn't need to remove the batch effect I mentioned. Thanks for your help.

Best,

Zhijie

Dr. Zhijie Han （韩智杰） Associate professor in Department of Bioinformatics School of Basic Medicine Chongqing Medical University, Chongqing, P.R. China @.***

      ------------------ Original ------------------ From: @.>; Date:  Mon, Aug 19, 2024 10:46 AM To: @.>; Cc: @.>; @.>; Subject:  Re: [Danko-Lab/BayesPrism] Can I used BayesPrism to perform deconvolution on the microarray results by the scRNAseq reference (Issue

96)

 

Dear user,

Thank you for your interest in our methods.

We have not tested if microarray data can be used as reference. We noted one recent study that applied BayesPrism to deconovovle the microarray bulk (https://www.biorxiv.org/content/10.1101/2023.06.14.544991v1.full), which seems to perform well. You may give it a try and see if the results make sense.

You may also try using markers when constructing the scRNA-seq reference to overcome the strong technical difference between RNA-seq and microarray data to see if it improves the results (provided you have some prior knowledge about the ground truth).

Best,

Tinyi

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

— Reply to this email directly, view it on GitHub https://github.com/Danko-Lab/BayesPrism/issues/96#issuecomment-2295667203, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB4NHS4I3RBD5SYTLYWUDWLZSF3BTAVCNFSM6AAAAABMR4ELWKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEOJVGY3DOMRQGM . You are receiving this because you commented.Message ID: @.***>