I would like to apply the limma gene set tests such as camera, romer etc to my RNAseq dataset which I have analysed in DESeq2. Am I right in thinking that the rlog transformed counts are the appropriate matrix to pass into these functions? I can't find a worked example anywhere that integrates these two workflows but apologies if I've missed it. Within EdgeR there are specific functions to pass a DGEList object to camera (edgeR::camera.DGEList) so I suppose a feature request for DESeq2 would be something similar, but certainly some guidance in the documentation on how to do this would also be welcomed!
Again, apologies if I've just missed the obvious.
Drug Discovery Unit, Cancer Research UK Manchester Institute