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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

`clusterProfiler`

makes use of a (fast) GSEA algorithm implemented in the package`fgsea`

(function`fgseaMultilevel`

). The warning is thus thrown by`fgsea`

, not`clusterProfiler`

.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 the`fgsea`

manuscript posted at bioRxiv, or maybe Alex (author`fgsea`

package) will chime in to explain... I don't know about the details...