i'm using deseq2 for my RNASeq analysis.
i have 2 factors, each has 2 levels:
1. genotype : col (wildtype), M6_5 (mutant)
2. treatment: Nacl, control
my design is: ~ genotype + treatment + treatment:genotype.
to get the effect of the treatment for each genotype i used:
results(dds, contrast = c("treatment","Nacl","control")
and to test differences between genotype on the same treatment conditions i used:
results(dds, contrast = c("genotype","M6_5","col")
results(dds, list(c("genotype_M6_5_vs_col","genotypeM6_5.treatmentNacl" ))
now, i'm looking for the comparison : M6_5 Nacl vs col control and M6_5 control vs col Nacl
is that possible using my design?
thanks a lot