Question: How to analyze RNAseq data with multiple treatment groups and each subject has pre and post-treatment measures using deseq2/edger/limma?
gravatar for wwu222
5 months ago by
wwu2220 wrote:


I am working on a set of RNAseq data that has the following design:

patients are randomized to different treatment groups: control, trt1 and trt2 each patient has pre and post treatment RNAseq data: time0 , time1

I am interested in getting treatment effect (not time effect). The model mentioned in DESeq2, edgeR and Limma helps to get time effect which is not the interest.

Any suggestion how to get treatment effect for RNAseq data with this design?

Thank you very much!

limma edger deseq2 tutorial • 210 views
ADD COMMENTlink written 5 months ago by wwu2220

Is this any different than the question you asked and the subsequent discussion that followed in this post?

ADD REPLYlink written 5 months ago by Steve Lianoglou12k

Same design, but this question is from broad perspective, not the detailed question regarding any problem with these packages. For example, what is the most appropriate way to address this question in high dimensional setting. Thanks!

ADD REPLYlink written 5 months ago by wwu2220

I don't have any additional comments from the previous post.

ADD REPLYlink written 5 months ago by Michael Love25k

Thank you, Dr. Love. You are always so nice!

ADD REPLYlink written 5 months ago by wwu2220
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