Hi Steffen, I have fixed the internal name issue and this change has now been pushed to the live ensembl servers. If I do the following query it seems to work: > library(biomaRt) > mymart = useMart("ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl", host="http://www.ensembl.org/biomart/martservice ") Checking attributes and filters ... ok > gene = c("XM_001124306") > getBM(attributes=c("refseq_dna_predicted", "ensembl_gene_id"), filters = "refseq_dna_predicted", values = gene, mart=mymart) refseq_dna_predicted ensembl_gene_id 1 XM_001124306 ENSG00000205358 > Hopefully it will therefore not be necessary for Becky to have to do an update. Regards, Rhoda On 12 Mar 2009, at 22:20, steffen at stat.Berkeley.EDU wrote: > Hi Becky, > > You query will work if you update biomaRt and use the developmental > version. > You can download it from here: > > http://bioconductor.org/packages/2.4/bioc/html/biomaRt.html > > You also need to specify what filter you are using, this seem to be > missing in your query. > > Once you've updated biomaRt try: > > ensembl<-useMart("ensembl", dataset="hsapiens_gene_ensembl") > > #use list filters to list the filternames > listFilters(ensembl) > > #then do you query using the correct attribute and filter name > > myGetBM <- > getBM(attributes=c("refseq_dna_predicted","ensembl_gene_id"), > filter="refseq_dna_predicted",values=genes, mart=ensembl) > > Cheers, > Steffen > >> Hi Becky, >> I have had a look at the Ensembl mart configuration and there are >> differences between the internal_name for the refseq dna predicted >> filter and attribute names. One has lowercase "dna" and the other has >> uppercase "DNA". I am in the process of fixing this and will let you >> know when it has been solved. Many thanks for reporting the bug and >> apologies for any inconvenience. >> Regards, >> Rhoda >> >> >> On 10 Mar 2009, at 16:26, Becky Saunders wrote: >> >>> Hi There, >>> >>> I have an error on Biomart where I can not use the >>> refseq_dna_predicted >>> attribute. >>> >>> If I use the following gene id data and the following commands I get >>> the >>> error: >>> >>>> genes >>> V1 >>> 1 XM_001000131 >>> 2 XM_001001115 >>> 3 XM_001001128 >>> 4 XM_001001137 >>> 5 XM_001002091 >>> 6 XM_001005165 >>> 7 XM_001005681 >>> 8 XM_001005979 >>> 9 XM_001006801 >>> 10 XM_001123368 >>> 11 XM_001123369 >>> 12 XM_001123374 >>> 13 XM_001123393 >>> 14 XM_001123395 >>> 15 XM_001123428 >>> 16 XM_001123478 >>> 17 XM_001124305 >>> 18 XM_001124623 >>> 19 XM_001124624 >>> 20 XM_001124630 >>> 21 XM_001124642 >>> 22 XM_001124651 >>> >>>> mart = useMart("ensembl") >>>> ensembl<-useDataset("hsapiens_gene_ensembl", mart=mart) >>> Checking attributes and filters ... ok >>>> myGetBM <- getBM(attributes=c("refseq_DNA_predicted", >>> "ensembl_gene_id"), values=genes, mart=ensembl) >>> >>> V1 >>> 1 Query ERROR: caught BioMart::Exception::Usage: Attribute >>> refseq_DNA_predicted NOT FOUND >>> Error in getBM(attributes = c("refseq_DNA_predicted", >>> "ensembl_gene_id"), : >>> Number of columns in the query result doesn't equal number of >>> attributes in query. This is probably an internal error, please >>> report. >>>> >>> >>> >>> Can anyone help? Basically I am just trying to map ensembl ids to >>> both >>> XM_ and NM_ RefSeq IDs. >>> >>> Many Thanks, >>> >>> Becky >>> >>> -- >>> >>> Dr Rebecca Saunders >>> >>> High Throughput Screening Laboratory - Cancer Research UK >>> >>> Tel No. +44 (0)207 269 3159 >>> >>> Fax No +44 (0) 207 269 3581 >>> >>> <http: www.cancerresearchuk.org=""/> >>> >>> >>> >>> This communication is from Cancer Research UK. Our website is at >>> www.cancerresearchuk.org >>> . We are a charity registered under number 1089464 and a company >>> limited by guarantee registered in England & Wales under number >>> 4325234. Our registered address is 61 Lincoln's Inn Fields, London >>> WC2A 3PX. Our central telephone number is 020 7242 0200. >>> >>> This communication and any attachments contain information which is >>> confidential and may also be privileged. It is for the exclusive >>> use of the intended recipient(s). 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Anyone >>> who communicates with us by e-mail is taken to accept the risks in >>> doing so. >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> Rhoda Kinsella Ph.D. >> Ensembl Bioinformatician, >> European Bioinformatics Institute (EMBL-EBI), >> Wellcome Trust Genome Campus, >> Hinxton >> Cambridge CB10 1SD, >> UK. >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > Rhoda Kinsella Ph.D. Ensembl Bioinformatician, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, UK.