no gene can be mapped (RNAseq analysis)

gseKEGG – no gene can be mapped (RNAseq analysis)

0

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:

enter image description here

Here is what my “res_entrez” object looks like

enter image description here


RNAseq


cluster-profiler


KEGG


GSEA

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