KEGGprofile: "Error in phyper - Non-numeric argument to mathematical function" when using non model organism
stefano romano <[email protected]> Sat, 13 Sep 2014 10:03:55 +0200
| Newsgroups | gmane.science.biology.informatics.conductor |
|---|---|
| Message-ID | <CAFL3zPYyGgHzW03bm=+9ArgfNwBtf-obN0Byu7r5-nQhicz_YQ@mail.gmail.com> |
Hi,
I am using KEGGprofile to perform KEGG enrichment for a non model organism.
Using the data from the R documentation i perfectely obtaine the enrichment.
>data(pho_sites_count)
>genes<-names(rev(sort(pho_sites_count[,1]))[1:300])
> summary(genes)
Length Class Mode
300 character character
> is.vector(genes)
[1] TRUE
>pho_KEGGresult<-find_enriched_pathway(genes,specis='hsa')
However, when I use my datasets, which I submit as character vector with
NCBI ID, I get the following error:
Error in phyper(kegg_result_length[x], keggpathway2gene_length[x],
length(unique(unlist(keggpathway2gene))) - :
Non-numeric argument to mathematical function
Any suggestion how to overcome this problem?
Thank you very much.
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