I am analyzing RNAseq data set with DESeq2. Samples are grouped in three groups: one control group (n=16) and two case groups (case 1 and 2, n=6 and n=8, respectively).
I want to find differentially expressed genes of both case groups against the control group, but also against each other (case1 vs case2).
When fitting a GLM, I can easily get the coefficients for case1_vs_control and case2_vs_control, and to compare case1 against case2, I could do case1_vs_control *vs* case2_vs_control, and that would produce differentially expressed genes whose log2FC over the control group differ between case1 and case2.
However, because of the degrees of freedom, I know a different result will come out if I directly compare case1 and case2, ignoring the control group. This also would require fitting another GLM for a two group comparison.
My question is which approach is more robust to compare case1 and case2.
Thanks in advance!