i did not find genesets my organism of interest in the search page of GSEA:

http://www.gsea-msigdb.org/gsea/msigdb/search.jsp

Can I use the pathawy genesets generated from the following code for GSEA:

pathways.list <- keggList("pathway", "pfa")


pathway.codes <- sub("path:", "", names(pathways.list)) 


genes.by.pathway <- sapply(pathway.codes,
                             function(pwid){
                             pw <- keggGet(pwid)
                             if (is.null(pw[[1]]$GENE)) return(NA)
                             pw2 <- pw[[1]]$GENE[c(TRUE,FALSE)]
                             pw2 <- unlist(lapply(strsplit(pw2, split = ";", fixed = T), function(x)x[1]))
                             return(pw2)})

Hi Mohammad,

Your organism of interest is Plasmodium falciparum? Yes, you can use GSEA against any gene-set, whether they be the curated gene sets from MSigDB, your own custom gene sets, or gene sets created from KEGG.

Which implementation of GSEA are you using? - fGSEA package?

Kevin