do expression of leading edges within a negative NES term reflect the same direction as it's enrichment score? aka downregulation of leading edges
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kavator ▴ 20
Last seen 15 months ago

Hi everyone; just want to double check my understanding of leading Edges in fgsea; according to FAQ of original gsea

"For a positive ES (such as the one shown here), the leading edge subset is the set of members that appear in the ranked list prior to the peak score. For a negative ES, it is the set of members that appear subsequent to the peak score."

so what i understand is that for positive NES; the expression values of leading Edges (the ones that drive the enrichment) follow the same direction of the ES ( upregulation) but for negative NES; the expression values of leading Edges are the opposite direction of the negative NES. Is my understanding correct?

Hope to hear some clarifications, thanks

fgsea • 350 views
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assaron ▴ 200
Last seen 5 weeks ago
St Petersburg

Yes, from a practical perspective, genes in the leading edge of up-regulated pathways (with positive ES) are also up-regulated, and for the down-regulated pathways they are also down-regulated.


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