Gene set enrichment analysis input data

Question

[ATCG]

I apologize for asking this naive question but I have read several tutorials and I feel unsure about the following: When using gene set enrichment analyses ( ReactomePA, clusterProfiler, gprofiler2 etc.) The input data is an order ranked geneList

1. Is this geneList the output from DESeq2 or a filtered list for example filtered by FDC or log2FoldChange?

2. This is how most tutorials filter the gene set in R:

   gene <- names(geneList)[abs(geneList) > 2]

Is this assigning the gene variable names of genes with values greater than the absolute value of 2?

Thanks!

Answer 1

[N15]

clusterProfiler does perform GSEA. For the kegg enrichment analysis, you start with a list of pathways or kegg genes (KOs) in your sample of interest compared to a background.

https://yulab-smu.github.io/clusterProfiler-book/chapter6.html#kegg-over-representation-test

[ATpoint]

I see, edited my comment, thanks.