Biomart with human genes NCBI 35/hg17
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Yan Jiao ▴ 140
@yan-jiao-4354
Last seen 8.1 years ago
Dear All, I'm trying to use the previous built (within Biomart)for human genes to get gene location, It seems like Ensembl 44 is the version I should use for NCBI 35/hg17, I did following: ensembl =useMart("ensembl_mart_44",archive=TRUE) listDatasets(ensembl) [1] dataset description version <0 rows> (or 0-length row.names) So you could see there is no dataset available, So if I do: ensembl =useMart("ensembl_mart_44",dataset="hsapiens_gene_ensembl",arc hive=TRUE) I got: Error in useDataset(mart = mart, dataset = dataset, verbose = verbose) : The given dataset: hsapiens_gene_ensembl , is not valid. Correct dataset names can be obtained with the listDatasets function. has anyone come across the same problem? Many thanks Yan [[alternative HTML version deleted]]
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@steffen-durinck-4465
Last seen 8.1 years ago
Hi Yan, Ensembl 44 is to far back and the BioMart interface has changed significanlty since, as a result you can't query such old archive. Any Ensembl version from Ensembl 52 and upwards should be fine though, unfortunately this won't help you as you want NCBI35, and Ensembl 52 is NCBI 36. Note that a better way to access the archives is to specifiy the host url as described in the vignette: ensembl54=useMart(host='may2009.archive.ensembl.org', biomart='ENSEMBL_MART_ENSEMBL', dataset='hsapiens_gene_ensembl') Cheers, Steffen On Tue, Jul 26, 2011 at 7:02 AM, Yan Jiao <y.jiao at="" ucl.ac.uk=""> wrote: > Dear All, > > > I'm trying to use the previous built (within Biomart)for human genes to get gene location, It seems like Ensembl 44 is the version I should use for NCBI 35/hg17, I did following: > > ensembl =useMart("ensembl_mart_44",archive=TRUE) > listDatasets(ensembl) > [1] dataset ? ? description version > <0 rows> (or 0-length row.names) > > So you could see there is no dataset available, > So if I do: > > ensembl =useMart("ensembl_mart_44",dataset="hsapiens_gene_ensembl",a rchive=TRUE) > I got: > Error in useDataset(mart = mart, dataset = dataset, verbose = verbose) : > ?The given dataset: ?hsapiens_gene_ensembl , is not valid. ?Correct dataset names can be obtained with the listDatasets function. > > has anyone come across the same problem? > > Many thanks > > Yan > > > ? ? ? ?[[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 >
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Hi Steffen, I also tried using lift genome annotations for mapping different built: http://genome.ucsc.edu/cgi-bin/hgLiftOver It helps a bit, but some regions it couldn't give me the mapping result, e.g. Failed input regions: #Split in new chr1:0-245500000 #Partially deleted in new chr21:0-46900000 I suppose the region is too long, any suggestions? Many thanks Yan -----Original Message----- From: Steffen Durinck [mailto:durinck.steffen@gene.com] Sent: 26 July 2011 15:52 To: Yan Jiao Cc: bioconductor at r-project.org Subject: Re: [BioC] Biomart with human genes NCBI 35/hg17 Hi Yan, Ensembl 44 is to far back and the BioMart interface has changed significanlty since, as a result you can't query such old archive. Any Ensembl version from Ensembl 52 and upwards should be fine though, unfortunately this won't help you as you want NCBI35, and Ensembl 52 is NCBI 36. Note that a better way to access the archives is to specifiy the host url as described in the vignette: ensembl54=useMart(host='may2009.archive.ensembl.org', biomart='ENSEMBL_MART_ENSEMBL', dataset='hsapiens_gene_ensembl') Cheers, Steffen On Tue, Jul 26, 2011 at 7:02 AM, Yan Jiao <y.jiao at="" ucl.ac.uk=""> wrote: > Dear All, > > > I'm trying to use the previous built (within Biomart)for human genes to get gene location, It seems like Ensembl 44 is the version I should use for NCBI 35/hg17, I did following: > > ensembl =useMart("ensembl_mart_44",archive=TRUE) > listDatasets(ensembl) > [1] dataset ? ? description version > <0 rows> (or 0-length row.names) > > So you could see there is no dataset available, > So if I do: > > ensembl =useMart("ensembl_mart_44",dataset="hsapiens_gene_ensembl",a rchive=TRUE) > I got: > Error in useDataset(mart = mart, dataset = dataset, verbose = verbose) : > ?The given dataset: ?hsapiens_gene_ensembl , is not valid. ?Correct dataset names can be obtained with the listDatasets function. > > has anyone come across the same problem? > > Many thanks > > Yan > > > ? ? ? ?[[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 >
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Heidi Dvinge ★ 2.0k
@heidi-dvinge-2195
Last seen 8.1 years ago
> Dear All, > > > I'm trying to use the previous built (within Biomart)for human genes to > get gene location, It seems like Ensembl 44 is the version I should use > for NCBI 35/hg17, I did following: > > ensembl =useMart("ensembl_mart_44",archive=TRUE) > listDatasets(ensembl) > [1] dataset description version > <0 rows> (or 0-length row.names) > Are you sure this is even available? If you check at http://www.ensembl.org/info/website/archives/index.html the closest they have there is 46, but that's already NCBI36. You might want to try contacting the Ensembl helpdesk directly. HTH \Heidi > So you could see there is no dataset available, > So if I do: > > ensembl > =useMart("ensembl_mart_44",dataset="hsapiens_gene_ensembl",archive=T RUE) > I got: > Error in useDataset(mart = mart, dataset = dataset, verbose = verbose) : > The given dataset: hsapiens_gene_ensembl , is not valid. Correct > dataset names can be obtained with the listDatasets function. > > has anyone come across the same problem? > > Many thanks > > Yan > > > [[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 >
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