gene set enrichment analysis- by enrichGO

Question

[CL]

Hey,

I ran DESeq and identified differentially expressed genes. I noticed that for running enrichment analysis, it's recommended to select genes with a fold change bigger than 2. My question is, do I also need to filter by p-value or p-adj? Is this necessary? I would like to get any suggestions.

Thanks!

Answer 1

[Istvan Albert]

Some analyses compare a subset of genes to a background. In those cases you would need to select a subset via some attributes like pvalues and or foldchanges.

Other types of enrichment analyses operate on ranked lists, in which case you don't need to filter your genes.