Thanks for the quick response! Best, Stefanie Am 03.05.2013 um 16:56 schrieb Steffen Durinck <durinck.steffen@gene.com>: > Hi Stefanie, > > Thank you for reporting this. The issue is that ENST00000594647 is a fairly new transcript id that was introduced in Ensembl 70. > By default you do your biomaRt queries to the central BioMart server which usually is quite good at updating it's Ensembl version whenever there is a new version of Ensembl (with about a 2 week lag). However at this time the BioMart server runs Ensembl 69 and the Ensembl database has had a new release last month to Ensembl 71. As ENST00000594647 was introduced in Ensembl 70 it doesn't return a result in version 69. > > Here's how you can query the current Ensembl version and get a result for this new transcript: > > ids = c("ENST00000594647","ENST00000335137") > > ensembl = useMart("ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl", host="www.ensembl.org") > > getBM(attributes=c("ensembl_transcript_id","external_gene_id"), values = ids, filters = "ensembl_transcript_id", mart = ensembl) > ensembl_transcript_id external_gene_id > 1 ENST00000335137 OR4F5 > 2 ENST00000594647 AL627309.2 > > I will contact the BioMart developers to check what the plan is to update the BioMart server to the latest version of Ensembl and report this back as a reply to this email. > > Cheers, > Steffen > > > > > > On Fri, May 3, 2013 at 5:23 AM, Stefanie Tauber <stefanie.tauber@univie.ac.at> wrote: > Dear list, > > I would like to retrieve some gene names for some ensembl transcript ids: > > library(biomaRt) > > > ids = c("ENST00000594647","ENST00000335137") > > > getBM(attributes=c("ensembl_transcript_id","external_gene_id"), values = ids, filters = "ensembl_transcript_id", mart = useMart("ensembl", dataset = "hsapiens_gene_ensembl")) > > 1 ENST00000335137 OR4F5 > > > Why don't I get a gene name for the first ID, which should be AL627309.2 according to: > > http://www.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;g=ENS G00000268020;r=1:53049-54936;t=ENST00000594647 > > ? > > > Best regards, > Stefanie > > > sessionInfo() > R version 3.0.0 beta (2013-03-24 r62391) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] de_AT.UTF-8/de_AT.UTF-8/de_AT.UTF-8/C/de_AT.UTF-8/de_AT.UTF-8 > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] biomaRt_2.15.1 GenomicFeatures_1.11.16 AnnotationDbi_1.21.16 > [4] Biobase_2.19.3 GenomicRanges_1.11.40 IRanges_1.17.41 > [7] BiocGenerics_0.5.6 > > loaded via a namespace (and not attached): > [1] Biostrings_2.27.12 bitops_1.0-5 BSgenome_1.27.1 > [4] DBI_0.2-5 RCurl_1.95-4.1 Rsamtools_1.11.27 > [7] RSQLite_0.11.2 rtracklayer_1.19.11 stats4_3.0.0 > [10] tools_3.0.0 XML_3.96-0.2 zlibbioc_1.5.0 > _______________________________________________ > 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 > DI Stefanie Tauber Center for Integrative Bioinformatics Vienna (CIBIV) (CIBIV is a joint institute of Vienna University and Medical University) Max F. Perutz Laboratories (MFPL) Campus Vienna Biocenter 5 (VBC5), Ebene 1, Room 1812.2 Dr. Bohr Gasse 9 A-1030 Wien, Austria Phone: ++43 +1 / 42772-4030 Fax: ++43 +1 / 42772-4098 email: stefanie.tauber@univie.ac.at www.cibiv.at [[alternative HTML version deleted]]