I have a question about an R-package: “ClusterProfiler”. There are two methods I’m using:
- gseKEGG (or gseGO, etc.)
- 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!