Question: gseGO: no term enriched under specific pvalueCutoff
0
gravatar for 14lwt1
11 weeks ago by
14lwt10
14lwt10 wrote:

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

clusterprofiler • 324 views
ADD COMMENTlink modified 7 days ago by rikki.frederiksen0 • written 11 weeks ago by 14lwt10

Hi 14lwt1,

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 pvalueCutoff seems to me to be non-functional.

ADD REPLYlink written 7 days ago by rikki.frederiksen0
0
gravatar for MatthewP
11 weeks ago by
MatthewP660
China
MatthewP660 wrote:

Your code is fine. You can try to set pvalueCutoff = 1 to get all possible results. You need to check your data at DESeq2 stage, for example, MA plot and vocanol plot, PCA or hclust to check sample distance.

ADD COMMENTlink written 11 weeks ago by MatthewP660

Thank you for the reply. Yea, I was just surprised that there isn't a significant result with that many genes as input. There are differences across the comparison based on sample distance.

ADD REPLYlink written 11 weeks ago by 14lwt10
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