Closed alexjacobsCDS closed 3 years ago
The p-value or adj p-value cutoff is used to filter the gene/proteins for geneset enrichment analysis, not the geneset enrichment p value. Geneset enrichment p-value is fixed at p < 0.05.
Understood, thank you! Closing this issue
We're seeing some strange behavior using the p-value cutoff on the Gene Set Enrichment tab. I'm not sure if maybe we're just confused about how this works. Is the p-value cutoff using the same p-value that's displayed in the gene set enrichment table? If so, I don't think it's working correctly. See the attached screenshot where row 14,15 are on opposite sides of the 'p-value cutoff'. If it's not using that p-value, what p-value is it using?
(this is using the demo mouse dataset included with the app)
Thanks!