Hi all, I have attempted to run gseGO as follows:
gseaResults <- gseGO(geneList = rankedList, OrgDb = org.Mm.eg.db, ont = "BP", nPerm = 1000, minGSSize = 10, maxGSSize = 500, pAdjustMethod = "BH", pvalueCutoff = 0.05, verbose = T, by = "fgsea")
Where, "rankedList" is a sorted double with logFCs named after EntrezIDs like so:
77583 234564 228802 11418 79235 21414 9.421894 9.089247 7.089965 6.471895 6.298729 6.141589
This includes 11234 genes in the results of DESeq2 after gene name conversion via bitr.
However, I could not get any result.
no term enriched under specific pvalueCutoff...
I have also tried it with ENSEMBL instead of ENTREZ. My clusterProfiler version is 3.14.3 and R is version 3.6.2.
I have the same issue. If I set the
pvalueCutoff = 1, then I get the full lists from which I can see that several biological processes do actually have pvalue<0.05. Hence, the argument
pvalueCutoffseems to me to be non-functional.
pvalueCutoffis use to filter