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.
Thank you