I was wondering whether anyone could shed light on this discrepancy I observed between two different edgeR versions.
I used a version 3.12.1 of edgeR and did all my gene set enrichment analysis with it, but recently I updated the edgeR version to 3.18 and realised that the p-values that were generated from using kegga() are different when v3.18 was used compared to when v3.12 was used.
It looks like the p-values were lower when v3.12 was used compared to v3.18, but the p-values from v3.18 seems to be closer to the actual p-values from fisher's exact test.
There was no difference in the input data and the parameters. Only difference is the edgeR version.
Any ideas (from the authors)? Thank you.