pathview error
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Fara • 0
Last seen 7 days ago

I am currently trying to conduct KEGG enrichment analysis using the Pathview package in R. However, R always responds with the following warning:

Warning: None of the genes or compounds mapped to the pathway! Argument gene.idtype or cpd.idtype may be wrong. 'select()' returned 1:1 mapping between keys and columns

Can you help me solve this problem?

This is the example of table. X1 is the gene name and X2 is the Log fold change. There are much more genes in the table.

#unlisting gene id and log fold change
Control_entrez_unlist_gene <-unlist(Control_entrez$NCBI.gene..formerly.Entrezgene..ID)
Control_entrez_unlist_fold = unlist(Control_entrez$Log.fold.change)

pathview_Control<- data.frame(matrix(ncol = 2, nrow = length(Control_entrez_unlist_gene)))

pathview_Control[1] = as.character(Control_entrez_unlist_gene)
pathview_Control[2] = Control_entrez_unlist_fold

pathview( = pathview_upregulated_PvsJControl, species = "dre", = "dre04672", limit = list(gene=2, cpd=1))
KEGGgraph KEGG • 195 views
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Last seen 15 hours ago
United States

The obvious would be to check that you have genes that map to that pathway. It's unusual to have so many NA values for your NCBI gene IDs, so you might check that as well.

Entering edit mode

Thank you for the reply.

I already conducted the KEGG enrichment analysis and I got the pathway ID.

So there is no doubt it cannot be mapped.

Also, the reason why I have so many NA values is that I converted the Ensembl ID to Entrez ID.

Will removing the NA values help solve the problem?

Entering edit mode

Will removing the NA values help solve the problem?

Did you try?

And, FWIW, in the cases I had ensembl-based RNA-seq datasets I removed all genes that had no corresponding entrezid before doing enrichment analysis. For that I used the ensembl-based annoation libraries (EnsDb), and not the OrgDb.


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