ClusterProfiler GSEA with geneList
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lucap • 0
@lucap-20484
Last seen 2.1 years ago

Hi everyone, Just a quick question. I want to perform GSEA on my geneList using clusterProfiler. Since I have a lot of genes and for some of them the logFC is small, I would like to perform GSEA only on the genes that have a logFC > 2. How do I do that in R?

I am following the recommended steps to prepare the geneList:

geneList = d[,2] names(geneList) = as.character(d[,1]) geneList = sort(geneList, decreasing = TRUE)

followed by:

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

but then I do not understand how to "filter" the gene list that will be submitted to GSEA? Maybe I am not supposed to do it, and I should only run GSEA with the whole geneList set? The code for GSEA I am using is:

kkGSEA <- gseKEGG(geneList=geneList, organism = "hsa", nPerm = 1000, pvalueCutoff = pvalue_gsea, minGSSize = 5)

Any help would be much much appreciated. Thanks :D

clusterProfiler GSEA geneList • 1.1k views
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@ludwig-geistlinger-3939
Last seen 25 days ago
USA/Boston/HMS

GSEA works on the full gene vector, testing whether genes of a gene set (here: a KEGG pathway) accumulate at the top or bottom of the full gene vector ordered by direction and magnitude of expression change.

If you are interested only in genes of significant expression change (here: abs(log2FC) > 2), and want to know whether certain gene sets (here: KEGG pathways) contain a disproportional number of these significant genes, you would rather carry out a over-representation analysis (ORA).

In clusterProfiler: use enrichKEGG for that purpose.

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Thanks Ludwig for the clear explanation! I see what you mean. I’ll carry the over-representation test then

Thanks Luca