Closed:Genelist input for ClusterProfiler

Question

[tbkuipers]

Hi everyone,

I have a question about an R-package: “ClusterProfiler”. There are two methods I’m using:

1. gseKEGG (or gseGO, etc.)
2. enrichKEGG (or enrichGO, etc.)

I can’t find an answer to what the exact input for these methods should be:

• For gseKEGG, I need a genelist with FC values, but does this genelist contain only DE genes? Or does this list contain all genes, DE and not DE (after filtering low expressed genes offcourse)?
• For enrichKEGG, I believe I only need the gene ID’s of DE genes, right?

I hope someone can help me out!

Tom