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interactivereport / Quickomics

Quickomics: exploring omics data in an intuitive, interactive and informative manner
https://quickomics.bxgenomics.com
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Strange p-value cutoff behavior on gene set enrichment #3

Closed alexjacobsCDS closed 3 years ago

alexjacobsCDS commented 3 years ago

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?

Screen Shot 2021-07-23 at 2 11 46 PM

(this is using the demo mouse dataset included with the app)

Thanks!

interactivereport commented 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.

alexjacobsCDS commented 3 years ago

Understood, thank you! Closing this issue