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Hi! I am trying to use the gseGo function in clusterprofiler for the first time. My code was as follows:
gse <- gseGO(geneList=geneList,
ont='ALL',
keyType = "ENSEMBL",
minGSSize = 3,
maxGSSize = 800,
pvalueCutoff = 0.05,
verbose = TRUE,
OrgDb = "org.Hs.eg.db",
pAdjustMethod = "hochberg")
I get this warning message:
In fgseaMultilevel (...) :
For some pathways, in reality P-values are less than 1e-10. You can set the 'eps' argument to zero for better estimation.
It seems like I'm being told I need to set it to 1e-10 but I'm unsure of what this actually means? I know that "This parameter sets the boundary for calculating the p value" but the p value of wether the pathway is enriched? Could anyone offer advice on this output/ a resource explaining it. TIA!
Under the hood
clusterProfilermakes use of a (fast) GSEA algorithm implemented in the packagefgsea(functionfgseaMultilevel). The warning is thus thrown byfgsea, notclusterProfiler.According to the tutorial page of
fgsea(here):In other words, setting the tuning constant
eps(epsilon) to zero (eps = 0) would increase the accuracy of the p-value calculations of the enriched gene sets. To check how this exactly works, you may want to have a look at thefgseamanuscript posted at bioRxiv, or maybe Alex (authorfgseapackage) will chime in to explain... I don't know about the details...