How to analyze RNAseq data with multiple treatment groups and each subject has pre and post-treatment measures using deseq2/edger/limma?

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wwu222 • 0

@wwu222-19179

Last seen 5.1 years ago

Hi,

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!

deseq2 limma edger Tutorial • 1.4k views

ADD COMMENT • link updated 5.1 years ago by Michael Love 41k • written 5.1 years ago by wwu222 • 0

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

https://support.bioconductor.org/p/116427/

ADD REPLY • link 5.1 years ago Steve Lianoglou ★ 13k

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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 REPLY • link 5.1 years ago wwu222 • 0

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

ADD REPLY • link 5.1 years ago Michael Love 41k

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

ADD REPLY • link 5.1 years ago wwu222 • 0

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