[BioC] error in gene2pathway results
mcarlson at fhcrc.org
Mon Mar 29 19:00:08 CEST 2010
It's not completely clear to me from you message how you got the gene id
19713, but if that is supposed to be an entrez gene, I note that it is
the entrez gene for the mouse version of RET. But in your code you
specified 'hsa', which is the 3 letter code from KEGG for humans.
On 03/29/2010 08:53 AM, Alberto Goldoni wrote:
> HI to everybody,
> i'm using the "gene2pathway" package but i'm not able to obtain something right.
> i'm using gene2pathway.signaltrans in order to predict a gene's
> membership to a KEGG signaling pathway and/or pathway component via
> the contained InterPro domains and in my case for the gene="19713",
> that represent RET proto oncogene
> But something is wrong as you can see down there....someone can help me?
>> pred.comp = gene2pathway.signaltrans("19713", organism = "hsa")
> Using KEGG information from SOAP service ...
> Mapping to signal transduction pathway components via KEGG database ...
> ---> Information found for 0 genes
> 1 genes to predict
> Retrieving information from InterPro database for organism ' hsa ' via
> Ensembl ...
> Checking attributes ... ok
> Checking filters ... ok
> Error in gene2pathway:::getInterProDomains(topredict, gene2Domains =
> gene2Domains, :
> No mapping Entrez gene ID -> InterPro found!
> Best regards.
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