Dear DESeq2 experts,
I have RNA-Seq data replicated from different genotypes. Let's say for the sake of example
sample genotype samp1 A samp2 A samp3 B samp4 B samp5 C samp6 C samp7 D samp8 D
and so on. I can easily compare each genotype against each other. Now let's say these genotypes have interesting common phenotypes (A and B have phenotype 1 and C and D have phenotype 2) and I want to compare combination of genotypes to find DEG that could explain the phenotypes. After reading DESeq2 vignette, manual, and several posts here and elsewhere, the only way I could think of to achieve this would be to write my condition file as :
sample phenotype samp1 1 samp2 1 samp3 1 samp4 1 samp5 2 samp6 2 samp7 2 samp8 2
then run the results function with contrast 2 versus 1. Can someone confirm this is the right and only way of doing it or am I missing something obvious here?