I'm hoping for some help modeling an RNA-Seq analysis in DeSeq2.
I have 4 populations (A,B,C,D) , and initially I used the following to compare them each to one another:
dds <- DESeqDataSetFromMatrix(countData = countData, colData = colData, design = ~ Experiment_Groups)
dds <- DESeq(dds, betaPrior = TRUE)
The above worked well finding AvsB, AvsC, AvsD, BvsC, BvsD, CvsD.
Now I'm interested in (A-B)-(C-D), is this possible in DeSeq2?
Would limma or ballgown be an alternative?
Thanks for your time.