[BioC] sequence_3utr_start and sequence_3utr_end

[Wolfgang Huber]

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 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:
> 
>> 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_IDENTIFICATION=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 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):
>>>
>> getBM(attributes=c('sequence_3utr_end'),filters='ensembl_gene_id',value="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
>>>