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]
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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
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--
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
--
