Differentail expression analysis between 3 groups

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3.1 years ago

adR ▴ 120

Hi, I have a question on differential expression analysis. I have 3 groups(A, B, C) and each group has 20 samples. I want to do differential expression analysis to get genes differently expressed in A, not in B and C. I would appreciate it if someone could give me some direction on this!

Best, AD

RNA-Seq DESeq2 limma DEA • 1.0k views

ADD COMMENT • link updated 3.1 years ago by Basti ★ 2.0k • written 3.1 years ago by adR ▴ 120

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What is the method you intend to use (i.e. which package ?) If you intend to use DESeq2, please see the "Contrasts" part of the vignette : https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html

ADD REPLY • link 3.1 years ago by Basti ★ 2.0k

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@basti, thank you for your answer. As far as I know, the contrast function in DESeq2 does compare between two groups (e.g A vs B, etc) but what I want to do is A vs B and C at the same time. So that I can get genes only expressed in A compared to B and C at time. I could use both packages as far as solving my problem.
Best, Amare