[BioC] sequence_3utr_start and sequence_3utr_end
huber at ebi.ac.uk
Tue Dec 16 19:21:37 CET 2008
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
Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber
12/12/2008 15:09 Javier Díez 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:
> R version 2.7.2 (2008-08-25)
> attached base packages:
>  stats graphics grDevices utils datasets methods base
> other attached packages:
>  RMySQL_0.6-0 DBI_0.2-4 biomaRt_1.14.1 RCurl_0.91-0
> loaded via a namespace (and not attached):
>  XML_1.93-2
> 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.
>> 1 Query ERROR: caught BioMart::Exception::Usage: Attribute 3utr_start NOT
>> 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?
>> 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.
>> --- On Fri, 12/12/08, Javier Díez <jdiezperezj at gmail.com> wrote:
>>> From: Javier Díez <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):
>>> but I got this error message:
>>> 1 Query ERROR: caught BioMart::Exception::Usage: Attribute
>>> 3utr_end NOT
>>> Any idea?
More information about the Bioconductor