I have been trying to extract the GSEA results from a list of genes after RNAseq analysis. It looks like my gseKEGG function is giving me problems. I am unable to generate a list of KEGG terms, it seems as my list of genes can't be mapped.
Could you help me please?
res_entrez <- dplyr::filter(res_ids, entrezid != "NA") res_entrez <- res_entrez[which(duplicated(res_entrez$entrezid) == F), ] foldchanges <- res_entrez$log2FoldChange names(foldchanges) <- res_entrez$entrezid foldchanges <- sort(foldchanges, decreasing = TRUE) set.seed(123456) gseaKEGG <- gseKEGG(geneList = foldchanges, organism = "mmu", nPerm = 1000, minGSSize = 20, pvalueCutoff = 0.05, verbose = FALSE) sessionInfo( )
This is the message I get when running the code:
Here is what my "res_entrez" object looks like.
I also tried the test with DOSE package, it seems to work and the geneList seems similar.
data(geneList, package="DOSE") kk2 <- gseKEGG(geneList = geneList, organism = 'hsa', minGSSize = 120, pvalueCutoff = 0.05, verbose = FALSE)
Here is what head of both geneList gives me
As input for
geneList = foldchanges, so you should show the content of that numeric vector (and not of
Also, as a side note, please use text, and do not paste pictures from R-studio... since that prevents easy copying of code or identifiers if needed.