sequence_3utr_start and sequence_3utr_end
2
0
Entering edit mode
Javier Díez ▴ 50
@javier-diez-2075
Last seen 9.6 years ago
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',valu e="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 [[alternative HTML version deleted]]
• 1.1k views
ADD COMMENT
0
Entering edit mode
@sean-davis-490
Last seen 12 weeks ago
United States
On Fri, Dec 12, 2008 at 7:58 AM, Javier D?ez <jdiezperezj at="" gmail.com=""> wrote: > 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',va lue="ENSG00000...",mart=mart) > > but I got this error message: > 1 Query ERROR: caught BioMart::Exception::Usage: Attribute 3utr_end NOT > FOUND > > Any idea? Hi, Javi. Could you provide a reproducible example and the output of sessionInfo()? Thanks, Sean
ADD COMMENT
0
Entering edit mode
@iain-gallagher-2532
Last seen 8.7 years ago
United Kingdom
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 Díez <jdiezperezj@gmail.com> wrote: > From: Javier Díez <jdiezperezj@gmail.com> > Subject: [BioC] sequence_3utr_start and sequence_3utr_end > To: bioconductor@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',va lue="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 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]
ADD COMMENT
0
Entering edit mode
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_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=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@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 Díez <jdiezperezj@gmail.com> wrote: > > > From: Javier Díez <jdiezperezj@gmail.com> > > Subject: [BioC] sequence_3utr_start and sequence_3utr_end > > To: bioconductor@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',va lue="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 > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]
ADD REPLY
0
Entering edit mode
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 >>>
ADD REPLY

Login before adding your answer.

Traffic: 946 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6