KYCG testEnrichmentSEA function appears to give biased z-scores (and p-values) that are stronger for positive estimates than negative ones.

[jdreyf]

We applied testEnrichmentSEA(z, databases = db, platform = "MM285", precise = TRUE) using sesame (v.1.24.0) for different databases where z is a vector of z-scores and found that positive estimates per DB in the output were given z-scores with larger absolute values and of course smaller p-values than negative estimates. So we tried testEnrichmentSEA(-1 * z, databases = db, platform = "MM285", precise = TRUE) to test the method, since I think it should be symmetric about positive vs. negative estimates. We found that the estimates did flip sign, but the z-scores, instead of flipping signs, were again biased toward having larger absolute value for positive estimates. So this appears to be a bug. We looked at the code and didn't find what caused the bug, though.

I also see that the devel branch no longer has the KYCG. I wonder if the database groups will still be kept somewhere, since we can still test the DB groups with other methods, e.g. Limma's pre-ranked Camera method, which is quick because it doesn't do any permutations.

Thanks for all your work on Sesame!
JD