Hi Reuben, it seems that BioMart Central that R is using is out of sync with Ensembl site. BioMart Central is on Ensembl 63 and Ensembl is already on 64.
Junjun: Please update the BioMart Central Server to 64 asap cheers, a On Thu, Sep 22, 2011 at 8:42 PM, Reuben Thomas <[email protected]>wrote: > Hello, > > I am trying to get information on a probes from the illumina_humanwg_6_v1 > platform using the R interface with the biomaRt library. For some reason, > some probes (around 1500) seem to no longer have any information on > ensembl. > > For example, "0004730161" is a probe with no information through this > interface, > > > getBM(attributes=c("illumina_humanwg_6_v1", "hgnc_symbol", "entrezgene"), > filters="illumina_humanwg_6_v1", values=c("0004730161"), uniqueRows=TRUE, > mart=ensembl) > > [1] illumina_humanwg_6_v1 hgnc_symbol entrezgene > > <0 rows> (or 0-length row.names) > > where as, "0006980528" is a probe that has information > > > getBM(attributes=c("illumina_humanwg_6_v1", "hgnc_symbol", "entrezgene"), > filters="illumina_humanwg_6_v1", values=c("0006980528"), uniqueRows=TRUE, > mart=ensembl) > > illumina_humanwg_6_v1 hgnc_symbol entrezgene > > 1 6980528 ATP10D 57205 > The BioMart web interface on the ensembl website however does provide > information for both these probes. > I am at a loss at trying to explain the missing probes from the biomaRt > R interface. Any help would be greatly appreciated. > Thanks, > Reuben Thomas > > > _______________________________________________ > Users mailing list > [email protected] > https://lists.biomart.org/mailman/listinfo/users > >
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