I have samples from 5 genotypes and 2 conditions. I am reading the 'Extract results from a DESeq analysis'
dds$genotype <- factor(rep(rep(c("I","II","III"),each=3),2)). But do not understand the 'each=3),2)' in this line, as I need to modify it for my 5 genotypes.
Also, I am interested in the effect that my treatment has in each genotype and don't have a reference genotype. Would it be better for me to use the group/factor rather than the interaction formula?