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

Question

[Shamim Sarhadi]

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?

Answer 1

[Benn]

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

[Shamim Sarhadi]

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