Hi,

I have a single factor (Treatment), three levels (Drug1, Drug2, Drug3)

dds <- DESeqDataSetFromMatrix(data, colData, design = ~ Treatment)
dds <- DESeq(dds)
results = results(dds)

If I want to get the DEG for Drug1 vs Drug2, I do:

results = results(dds, contrast = c("Treatment" , "Drug1" , "Drug2"))

Drug2 vs Drug3, I do:

results = results(dds, contrast = c("Treatment" , "Drug2" , "Drug3"))

But how to do Drug1 vs (Drug2 + Drug3) ?

Should I create a new factor (ex: MixTreatment) with 2 levels Drug1, DrugMix = (Drug2 + Drug3) and then do:

results = results(dds, contrast = c("MixTreatment" , "DrugMix"))

or alternative approach ?

Thanks,

See DESeq2: Compare expression of one group to the mean of others, DESeq2: Comparing one sample with the mean of all for testing against an average. Many other threads if searching for "deseq2 test average".