I do have a project with the exact same design as in the DESEQ2 manual under "Group-specific condition effect". Meaning I have two groups of diseased animals, one group treated with drug 1 (2 timepoints: baseline and treated) and one group treated with drug2 (different individuals in each group).
So I was pretty much following the manual, however the whole thing is quite complex for my limited understanding.
My main question is how to phrase it what the differentially expressed genes represent?
my results() call looks as follows: resGroup<-results(dds, contrast=list("TreatmentDrug2.Timepointtreated","TreatmentDrug1.Timepointtreated"))
Is this reasonable? And how would I describe what the diff. expressed genes represent? What about something along the lines of: Genes that are responding differently to the two treatments, taking into account the intra-individual effect? (And would a log2fold change of +2 mean that the expression is accordingly higher in drug2 compared to drug1; taking into account effect of individuals)?
Thanks a lot and merry christmas!