Gene set enrichment analysis input data
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19 months ago
ATCG ▴ 360

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!

GSE DESeq2 • 1.1k views
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Entering edit mode
19 months ago
N15 ▴ 160

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

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I see, edited my comment, thanks.

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