How can I get gseGO to return all GO terms tested?
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yesitsjess • 0
@yesitsjess-11565
Last seen 5 weeks ago
United Kingdom

Can I return a result for every GO term tested? I'd hoped increasing the p value to 1 would mean no results would be filtered out but it doesn't seem to have worked that way.

geneList below is a vector of fold changes with ensembl IDs as names

      gsea_res <- gseGO(geneList=geneList, OrgDb=org.Hs.eg.db, keyType="ENSEMBL", ont="BP", pAdjustMethod="BH", minGSSize=100, maxGSSize=500, pvalueCutoff=1)
clusterProfiler clusterp • 162 views
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@james-w-macdonald-5106
Last seen 2 hours ago
United States

Seems to work OK?

> library(clusterProfiler)
> library(org.Hs.eg.db)
> data(geneList, package = "DOSE")
> z <- gseGO(geneList, "BP", org.Hs.eg.db, pvalueCutoff = 1)
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
Warning message:
In fgseaMultilevel(pathways = pathways, stats = stats, minSize = minSize,  :
  For some pathways, in reality P-values are less than 1e-10. You can set the `eps` argument to zero for better estimation.
> zz <- gseGO(geneList, "BP", org.Hs.eg.db)
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
Warning message:
In fgseaMultilevel(pathways = pathways, stats = stats, minSize = minSize,  :
  For some pathways, in reality P-values are less than 1e-10. You can set the `eps` argument to zero for better estimation.
> summary(z$pvalue)
   Min. 1st Qu.  Median    Mean 
0.00000 0.04104 0.24027 0.33392 
3rd Qu.    Max. 
0.58711 1.00000 
> summary(zz$pvalue)
     Min.   1st Qu.    Median 
0.000e+00 9.487e-06 5.611e-04 
     Mean   3rd Qu.      Max. 
1.450e-03 2.417e-03 6.513e-03 
> length(z$ID)
[1] 5777
> length(zz$ID)
[1] 753

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