gseKEGG - no gene can be mapped (RNAseq analysis)
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0
Entering edit mode
redafazazi • 0
@90e8f417
Last seen 14 months ago
Canada

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)

sessionInfo( )

This is the message I get when running the code:

enter image description here

Here is what my "res_entrez" object looks like. enter image description here

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

enter image description here

KEGG clusterProfiler • 4.6k views
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1
Entering edit mode

As input for gseKEGG you used geneList = foldchanges, so you should show the content of that numeric vector (and not of res_entrez nor foldchanges_sex!).

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.

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3
Entering edit mode
Erqiang Hu ▴ 50
@13766876214-21289
Last seen 3 months ago
Guangzhou

It has been solved by the lastest version of clusterProfiler in Github. See https://github.com/YuLab-SMU/clusterProfiler/issues/542 and https://github.com/YuLab-SMU/clusterProfiler/pull/540.

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