gseGO: no term enriched under specific pvalueCutoff
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Entering edit mode
2.9 years ago
14lwt1 • 0

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,
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 • 5.9k views
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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.

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pvalueCutoff is use to filter pvalue and p.adjust.

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Entering edit mode
2.9 years ago
MatthewP ★ 1.2k

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.

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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.