Hi all,

I have a situation like WT, KO, WT+DRUG, KO+DRUG (5 replicates each). The initial idea to do the pair wise comparison and i did it. I have the results for WT vs KO and WT+DRUG, vs KO+DRUG. But i would like to run DESEQ2 with interaction term. would it be vice if i consider WT vs KO as genotype-1 and WT+DRUG, vs KO+DRUG as a genotype-2. And my formula is

design(dds) <- ~ genotype + condition + genotype:condition

Or do i have to change.

With the right results call, this should return what you want.