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A rational way for selecting the number of DEG with significant p-value for GSEA

suppose I have 1000 prob-id(output of the limma) with the significant p-value, should all of them be select for GSEA, or there is a rational way of choosing the number of DEG for GSEA?

deg gsea
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updated by Benn Benn • written by Shamim Sarhadi Shamim Sarhadi

1 answer

Give it a try and see if it makes sense. If not, you can also try up and down regulated genes separately.

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written by Benn Benn

something like trial and error approach !!! thank you b.nota

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written by Shamim Sarhadi Shamim Sarhadi

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