I learnt from the this old post (limma roast syntax for overall anova) that ROAST cannot be performed on multiple contrasts (i.e., with the F-test). This is still true, I suppose? In that post it was suggested to use
geneSetTest with Fstatistic (from
First, my understanding was that
geneSetTest test different hypotheses, i.e., self-contained vs competitive. So this is not exactly apples and apples, is it?
Second, there is also
cameraPR now available in limma. What is the recommendation for using
cameraPR? In my analysis, I get very good significance (p<0.001) with
geneSetTest and no significance (p>0.5) with
cameraPR (once the inter gene correlation is included). I would like to know which to believe/interpret.
Third, more generally, in my analyses, I find situations where I apply either
camera on a single gene set, I get discordant conclusions. I understand they test different hypotheses. I do not want to indulge in p-value hacking and pick the test that fits my story. So do you have suggestions as to how to go about this in a consistent manner. (as an aside, I can suggest an explanation for no significance in
ROAST but significance in
CAMERA, when the effects are so small and limited to be insignificant overall due to multiple testing, but gene set of interest has all the genes on which there is some effect).