biomart database version problem
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lemon tree ▴ 40
@lemon-tree-5473
Last seen 7.1 years ago
Dear All, Recently, I found the mouse gene annotation in biomart had been changed to the version GRCm38 (mm10). However, I want to use mm9 version. Could anyone give some suggestions about how to do this? My code is mart <- useMart(biomart="ensembl",dataset="mmusculus_gene_ensembl") Thanks! Best all! David! [[alternative HTML version deleted]]
Annotation biomaRt Annotation biomaRt • 2.6k views
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@steffen-durinck-4465
Last seen 7.1 years ago
Hi David, This should get you there: mart = useMart('ENSEMBL_MART_ENSEMBL',dataset='mmusculus_gene_ensembl', host="may2012.archive.ensembl.org") Cheers, Steffen On Wed, Aug 29, 2012 at 10:10 AM, lemon tree <lemon.wang218@gmail.com>wrote: > Dear All, > Recently, I found the mouse gene annotation in biomart had been changed > to the version GRCm38 (mm10). However, I want to use mm9 version. > Could anyone give some suggestions about how to do this? My code is > mart <- useMart(biomart="ensembl",dataset="mmusculus_gene_ensembl") > > Thanks! > > Best all! > > David! > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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Thanks very much! David Wang. On Wed, Aug 29, 2012 at 12:23 PM, Steffen Durinck <durinck.steffen@gene.com>wrote: > Hi David, > > This should get you there: > > mart = useMart('ENSEMBL_MART_ENSEMBL',dataset='mmusculus_gene_ensembl', > host="may2012.archive.ensembl.org") > > Cheers, > Steffen > > > > On Wed, Aug 29, 2012 at 10:10 AM, lemon tree <lemon.wang218@gmail.com>wrote: > >> Dear All, >> Recently, I found the mouse gene annotation in biomart had been changed >> to the version GRCm38 (mm10). However, I want to use mm9 version. >> Could anyone give some suggestions about how to do this? My code is >> mart <- useMart(biomart="ensembl",dataset="mmusculus_gene_ensembl") >> >> Thanks! >> >> Best all! >> >> David! >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]]
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@james-w-macdonald-5106
Last seen 17 hours ago
United States
Hi David, From ?useMart I see archive: Boolean to indicate if you want to access archived versions of BioMart databases. Note that this gives access to only a limited number of archived BioMarts and the most recent archives are often not available. A better alternative is to leave archive = FALSE and to specify the url of the archived BioMart you want to access see vignette for an example. and if I then look at the vignette I see that this is outlined clearly on pages 14-15. Best, Jim On 8/29/2012 1:10 PM, lemon tree wrote: > Dear All, > Recently, I found the mouse gene annotation in biomart had been changed > to the version GRCm38 (mm10). However, I want to use mm9 version. > Could anyone give some suggestions about how to do this? My code is > mart<- useMart(biomart="ensembl",dataset="mmusculus_gene_ensembl") > > Thanks! > > Best all! > > David! > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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