Hi, This is a temporary problem to be resolved. For now use the getBM function to retrieve gene information from species other than homo sapiens.
Cheers, Steffen > Hi > I still cannot use the getGene function with other species than homo > sapiens. Is this function specific to homo sapiens or is it a problem > which is to be solved. > thanks > > TM > > Arek Kasprzyk a écrit : >> >> On 18 May 2006, at 09:29, TM wrote: >> >>> Hi >>> using the getGene function with hsapiens return result but now that >>> i'm using the mmusculus specie it doesn't work >>> for example with a mmusculus refseq : >>>> martMm <- useMart(biomart = "ensembl", >>>> dataset="mmusculus_gene_ensembl") >>>> getGene(id = "NM_019695", type = "refseq", mart = martMm) >>>> Error in getBM(attributes = c(att, "hgnc_symbol", "description", >>>> chrname, : >>>> attribute: hgnc_symbol not found, please use the function >>>> 'listAttributes' to get valid attribute names >>> >> >> Hi Tabare, >> you need an expert advice on this but from the naming there I can guess >> that hgnc_symbol is >> not applicable for mouse - these are human identifiers so the function >> there probably resolves >> to the non-existent mouse attribute >> >> >> a. >> >> >>> whereas with a hsapiens refseq it gives result and no error message: >>>> martHs <- useMart(biomart = "ensembl", >>>> dataset="hsapiens_gene_ensembl") >>>> getGene(id = "NM_000015", type = "refseq", mart = martHs) >>> >>> Can anyone tell me what I'm doing wrong? is this function just for >>> homo sapiens ? >>> Thanks >>> >>> Tabaré Mourot >>> >>> -- MOUROT Tabaré >>> Stagiaire Master Pro BioInfo >>> Plateforme transcriptome >>> Institut de Génomique Fonctionnelle >>> 141, rue de la Cardonille >>> 34094 Montpellier Cedex 5 >>> >>> Tel : +33 (0)4 67 14 29 64 >>> E-mail : [EMAIL PROTECTED] >>> >>> -- Passerelle antivirus IGF >>> -- >>> >>> >> >> >> ------------------------------------------------------------------------------- >> >> Arek Kasprzyk >> EMBL-European Bioinformatics Institute. >> Wellcome Trust Genome Campus, Hinxton, >> Cambridge CB10 1SD, UK. >> Tel: +44-(0)1223-494606 >> Fax: +44-(0)1223-494468 >> ------------------------------------------------------------------------------- >> >> >> >> >> >> --Passerelle antivirus IGF >> -- >> > > -- > MOUROT Tabaré > Stagiaire Master Pro BioInfo > Plateforme transcriptome > Institut de Génomique Fonctionnelle > 141, rue de la Cardonille > 34094 Montpellier Cedex 5 > > Tel : +33 (0)4 67 14 29 64 > E-mail : [EMAIL PROTECTED] > > -- > Passerelle antivirus IGF > -- > >
