I have a RNA-seq dataset with the following design and I want to find how
Treatment is affected by the
the samples belong to.
From the vignette, I understand that my design needs to be:
and the results are given by
design(dds) <- ~ Group + Treatment + Group:Treatment dds <- DESeq(dds) resultsNames(dds)
the Treatment effect for Group A:
res1=results(dds, contrast=c("Treatment", "B", "A"))
the Treatment effect for Group B:
res2=results(dds, list( c("Treatment_B_vs_A", "GroupB.TreatmentB") ))
the interaction term, answering: is the Treatment effect different across groups?
What I wanted to ask is how one can interpret the results in
res3 and whether they would be the same if I prepare a Venn diagram