Dear Bioconductor community,
I'm looking for gene set analysis tests that produce a quantitative value for each set and sample/comparison along with a p-value and are designed (or at least have proven to perform well) for focused gene set testing with 2 custom gene sets. Further, I'm looking for tests that work with datasets composed of several sample groups with only a few replicates per sample group. So far it seems like ROAST, CAMERA, SAM-GS, and GlobalTest might work well for my study. Any suggestions regarding these tests or other tests that might work would be appeciated.