Question: GSEA using clusterProfiler
gravatar for dxc008263
13 months ago by
dxc0082630 wrote:

Hi, I am trying to do GSEA with clusterProfiler using gseKEGG function. However, I keep getting this error:

preparing geneSet collections... --> Expected input gene ID: 18639,11997,74551,18642,104112,18640 Error in check_gene_id(geneList, geneSets) : --> No gene can be mapped....

This is what I did. I sorted my gene list first:

GSEAList <- sort(WTvsKoBasal,decreasing = TRUE) head(GSEAList) Gene.Id112 Gene.Id264 Gene.Id156 Gene.Id121 Gene.Id177 Gene.Id403 "99899" "99543" "98365" "97114" "97086" "94284"

Then I ran this command:

WTvsKOBasalGSEA<-gseKEGG(geneList = GSEAList, organism = "mmu", keyType = "kegg", exponent = 1).

Then I will get an error as I mentioned in the beginning.

Any suggestion will be appreciated!



ADD COMMENTlink modified 13 months ago • written 13 months ago by dxc0082630

Maybe you have your IDs as numbers - clusterProfiler expects them to be characters.

ADD REPLYlink written 13 months ago by mkulecka310

can you provide a sample of your gene ids that you are supplying to gseKEGG()

ADD REPLYlink written 9 months ago by xenon10
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