Hi,
I'm using the biomaRt package in R to query gene transcripts from "Ensembl Genes
61; Mus Musculus NCBIM37". Unfortunately I obtain different results depending on
which biomart-service I'm using. Here's an example:
defaultMart = useDataset("mmusculus_gene_ensembl", mart = useMart("ensembl"))
ensemblMart <- useMart("ENSEMBL_MART_ENSEMBL", dataset =
"mmusculus_gene_ensembl", host = "www.ensembl.org", path =
"/biomart/martservice", archive = FALSE)
getBM(attributes=c('ensembl_gene_id', 'ensembl_transcript_id'),
filters=c('ensembl_gene_id'), values=c('ENSMUSG00000047507'),mart=defaultMart);
ensembl_gene_id ensembl_transcript_id
1 ENSMUSG00000047507 ENSMUST00000056357
getBM(attributes=c('ensembl_gene_id', 'ensembl_transcript_id'),
filters=c('ensembl_gene_id'), values=c('ENSMUSG00000047507'),mart=ensemblMart);
ensembl_gene_id ensembl_transcript_id
1 ENSMUSG00000047507 ENSMUST00000056357
2 ENSMUSG00000047507 ENSMUST00000169109
So obviously one transcript is missing when using the default mart.
It looks to me that the biomart-service is not in sync with ensembl, because if
I use the archive mirror 'nov2010.archive.ensembl.org' the ensembl results match
the biomart.org results. Is there a sync-schedule available? Or is there another
reason for the mismatch?
Best, Holger Brandl
--
Dr. Holger Brandl
Bioinformatics Service
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 Dresden, Germany
Tel.: +49/351/210-2738
Fax: +49 351 210 2000
www: http://www.mpi-cbg.de
_______________________________________________
Users mailing list
[email protected]
https://lists.biomart.org/mailman/listinfo/users
