Hi, I need a little guidance on the interpretation of multi-factor analyses.

I have the factors Stage (Q & W) + Treatment (treated & control)

I created the dds object with:

ddsT <- DESeqDataSetFromMatrix(countData = counts, colData = Design, design = ~Stage + Treatment + Stage:Treatment) ddsT <- DESeq(ddsT)

resultsNames(ddsT) [1] "Intercept" "StageWvsQ" [3] "Treatmenttreatedvscontrol" "StageW.Treatmenttreated"

If I calculate:

results(ddsT, name = "StageWvs_Q" )

This will give me the comparison of Q vs W for Treatment condition - control, is that correct?

so then:

results(ddsT, name = "Treatmenttreatedvs_control" ) #--> treated v control for Q?

to get Q v W for treated (rather than control) would I need to do this:

results(ddsT, contrast = list(c("StageWvs_Q","StageW.Treatmenttreated"))) ?

and for treated v control within W:

results(ddsT, contrast = list(c("Treatmenttreatedvs_control","StageW.Treatmenttreated"))) ?

Thank you for any tips, Mark

Take a look at the examples in ?results.

We spell all of the comparison out there.

There’s also a diagram in the vignette