Combining NES and FDR q-values over gene set clusters (Enrichmentmap) in GSEA
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4 months ago
lsy9 ▴ 10

I have run GSEA and clustered overlapping gene sets using Enrichmentmap app in Cytoscape. I have too many significant gene sets and want to show how much they changed (NES) in a more summarized way. (I have already collapsed the clusters to a node in the network figure, but I want to also show the numbers ) Can I simply average the NES values for each cluster?

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+I have collapsed each cluster to a meta-node using Autoannotate app. Now, when I click a meta-node, the node table shows 'arithmetic mean of NESs' and 'arithmetic mean of FDR q-values' over all gene sets included in that cluster.

Can I simply report these values? I'm confused because I only know basic statistics and I'm not sure if I can combine p-values (and NES) in this way.

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