I am still quite new to DESeq2 and I would like to ask whether what I am doing is really what I WANT to do. My problem looks like this: I have two genotypes (I and II) and two conditions (A and B). I want to make a comparison of comparisons that should look like this:
(IIB vs IB) vs (IIA vs IA)
What I am doing currently is the following:
dds <- DESeqDataSetFromMatrix(countData = cts, colData = coldata, design = ~genotype + condition + genotype:condition) dds <- DESeq(dds) res <- results(dds, contrast=list("genotypeII.conditionB", "genotype_II_vs_I"))
From what I was reading in the DEseq2 manual I assume that "genotypeII.conditionB" corresponds to the (IIB vs IB) comparison that I want to make and "genotype_II_vs_I" corresponds to (IIA vs IA). I would be very glad if someone could tell me if that is correct and if not maybe point me to the correct way to do it.
Thanks for the help!