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GSEA test

Hi everyone, I'm trying to test and interpret some GSEA result (e.g. 100 genes between grA and grB).

Usually, when we use some carefully designed gene sets on public database, the graph will be in a bell-like shape. If it is left-up skew -> upregulated in grA (down in grB), right-down skew -> Up in grB (down in grA).

So, my question is, what if I input my own genes set, and 90% them are not expressed (zero count in alignment), then my GSEA graph will be all way down (no bell shape). So the interpreted result will be "wrong gene set", or "gene set is downregulated in GrA"?

enrichment gsea single-cell
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written by jackson9 • jackson9

You should not include non-expressed genes as their ranking is arbitrary and by this adds noise.

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written by ATpoint ATpoint

But if I want to test a pathway, which includes lots of non-expressed genes, then what will be the right conclusion?

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written by jackson9 • jackson9

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