gseKEGG – no gene can be mapped (RNAseq analysis)
Hi all,
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)
I obtain the error message:
Here is what my “res_entrez” object looks like
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