Differentail expression analysis between 3 groups
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
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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
@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
This might help you : DEseq three-group comparison