gravatar for tbkuipers

2 hours ago by

Netherlands/Leiden

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



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