DESeq2 multiple group comparisons
I have a column with a "group" variable in two datasets. In dataset#1 I have three types (A, B, C) within the group variable, and in dataset#2, I have four types (A, B, C, D). I want to perform Differential Expression for all three and four types, respectively, using DESeq2 such that I can assign up-regulated genes specific to each type.
I tried doing the pairwise comparisons for dataset#1 as follows:
A vs B
B vs C
C vs A
And then took the up-regulated genes specific to type A, B, and C.
Now, I am wondering if instead I create a new variable and perform Differential Expression to be able to identify DE genes specific to each type as follows:
A vs BandC
B vs CandA
C vs AandB
Is it the right way to go about it? Also, can I do so such a comparison with four types as well? Your suggestions are highly appreciated. Thanks!
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