Dear Javier if you would like help, then you might want to be more specific than "it does not work." As Sean suggested, can you give us a reproducible example? Also, please try with a current version of R and biomaRt. Since biomaRt is talking to an online webservice, BioMart, which is under active development, you will be happier if you use an equally up-to-date biomaRt client. -- Best wishes Wolfgang ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber 12/12/2008 15:09 Javier D?ez scripsit > Hi Iain, > Thanks for forwarding the reply. > According to the reply it should work now (52 is the current release, > doesn't it? ) but it does not, have you check if it is already working for > you ? > That is the output of session info: > >> sessionInfo() > R version 2.7.2 (2008-08-25) > x86_64-pc-linux-gnu > > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_ US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC _NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDEN TIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] RMySQL_0.6-0 DBI_0.2-4 biomaRt_1.14.1 RCurl_0.91-0 > > loaded via a namespace (and not attached): > [1] XML_1.93-2 > > Best > > Javi > > > On Fri, Dec 12, 2008 at 3:06 PM, Iain Gallagher < > iaingallagher at btopenworld.com> wrote: > >> Hi Javier. >> >> You might find the following exchange between myself and the ENSEMBL help >> desk last week useful. >> >> First my email: >> >> Using biomaRt through R to try and retrieve the 3'UTR start and end for a >> set of transcript ids I get the following error. >> >> V1 >> 1 Query ERROR: caught BioMart::Exception::Usage: Attribute 3utr_start NOT >> FOUND >> Error in getBM(attributes = c("ensembl_transcript_id", >> "sequence_3utr_start"), : >> Number of columns in the query result doesn't equal number of attributes in >> query. This is probably an internal error, please report. >> >> Could you tell me the easiest way to get hold of the 3'utr coordinates >> through the web interface please? >> >> Thanks >> >> Iain >> >> And the reply: >> >> >> Hello Iain, >> >> Currently these attributes are not available from BioMart. They have >> been dropped when we moved to an automated Mart building process a few >> months ago. However, as many people have asked for these attributes, >> they have been added again to our v52 release which, if everything goes >> according to plan, should go live coming week. My apologies for any >> inconvenience caused. >> >> >> >> Hope that helps. >> >> Iain >> >> >> --- On Fri, 12/12/08, Javier D?ez <jdiezperezj at="" gmail.com=""> wrote: >> >>> From: Javier D?ez <jdiezperezj at="" gmail.com=""> >>> Subject: [BioC] sequence_3utr_start and sequence_3utr_end >>> To: bioconductor at stat.math.ethz.ch >>> Date: Friday, 12 December, 2008, 12:58 PM >>> Hi everyone, >>> >>> I have tried this query (just to get the 3 utr coordinates >>> of transcripts of >>> a given gene): >>> >> getBM(attributes=c('sequence_3utr_end'),filters='ensembl_gene_id',v alue="ENSG00000...",mart=mart) >>> but I got this error message: >>> 1 Query ERROR: caught BioMart::Exception::Usage: Attribute >>> 3utr_end NOT >>> FOUND >>> >>> Any idea? >>> >>> Thanks >>> >>> Javi >>>