Comparing two conditions within multiple different groups with unequal sizes in DESeq
I have two conditions (condition A and condition B) and 4 groups (group 1, group 2, group 3).
I want to compare condition A to condition B within each of the groups, performing differential expression analysis using DESeq2. Then I want to contrast the results between groups, to determine which genes are uniquely differentially expressed in each group.
My problem is that my group sizes are very unequal:
Group 1: 37 x condition A; 50 x condition B
Group 2: 14 x condition A; 33 x condition B
Group 3: 5 x condition A; 5 x condition B.
I was wondering whether it is recommended to use DESeq2 as normal in this instance, using adjusted p-values and LFC values, or whether it is recommended to obtain the standardized effect sizes or something similar? I am concerned that I will obtain a falsely large number of SDE genes for group 1 compared to group 2 and 3 as a result of the much larger sample size in group 1.
Many thanks in advance for any tips that anyone has!
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