[BioC] KEGGprofile: "Error in phyper - Non-numeric argument to mathematical function" when using non model organism

[zhao shilin]

Dear Stafano,

I think the ID from the non model organism may cause the error. Would you
please tell me the specie you tested and send me some of your genes. So
that I can have a try.
Thank you!

Best,
Shilin

2014-09-13 3:03 GMT-05:00 stefano romano <stfn.romano at 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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