gravatar for 14lwt1

2 hours ago by

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

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modified 1 hour ago

by

MatthewP510

written
2 hours ago
by

14lwt10



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