Yes, we are in the process of preparing Ensembl 64. Junjun Sent from my BBerry
From: Arek Kasprzyk [mailto:[email protected]] Sent: Thursday, September 22, 2011 08:56 PM To: Reuben Thomas <[email protected]> Cc: [email protected] <[email protected]> Subject: Re: [BioMart Users] Missing Illumina Probe Ids when using biomaRt 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]<mailto:[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]<mailto:[email protected]> https://lists.biomart.org/mailman/listinfo/users
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