On Sat, May 29, 2010 at 1:11 AM, <mauede@alice.it> wrote:

>  Actually, the same query has worked with a smaller number of ENST...many
> times for me too.
>  But if the length of the filtering vector is really the problem then I
> feel confused.

 Some months ago I was extracting one UTR sequence at a time, thus keeping
>  the connection to biomaRt opened for several hours. At that time biomaRt
> was cutting me off
>  after some time (of variable length).  I posted my question to
> Bioconductor asking why biomaRt
>  was kicking me out. I was strongly adviced to downloasd all needed data
> all together with
>  one single query and then parse the downloaded stuff off-line.
>  If I got it right now you suggest downloading a few data at a time.
>  I'd really appreciate knowing whether there are limits in the amount of
> data that can be requested
>  in a query and, if so,  the upper boud.
>

Hi, Maura.  The length of the query is not the issue, I do not think.  I
would suggest following the lead of the package author and include the
output of sessionInfo() and send him the list of ENST ids as a .Rda or .txt
file.  That will be the quickest way of getting an answer to your problem.

Sean


> -----Messaggio originale-----
> Da: michael watson (IAH-C) [mailto:michael.watson@bbsrc.ac.uk]
> Inviato: ven 28/05/2010 22.54
> A: mauede@alice.it; Bioconductor  List
> Oggetto: RE: [BioC] why biomaRt cannot extract 3UTR sequences for 1941
> ENSGxxxxx        ?
>
> The following (small) code works for me:
>
> library(biomaRt)
> mart <- useMart("ensembl","hsapiens_gene_ensembl")
> ids <- c("ENST00000262187","ENST00000296271")
> seq <- getSequence(id=ids, type="ensembl_transcript_id", mart=mart,
> seqType="3utr")
> seq
> ________________________________________
> From: bioconductor-bounces@stat.math.ethz.ch [
> bioconductor-bounces@stat.math.ethz.ch] On Behalf Of mauede@alice.it [
> mauede@alice.it]
> Sent: 28 May 2010 21:41
> To: Bioconductor  List
> Subject: [BioC] why biomaRt cannot extract 3UTR sequences for 1941
> ENSGxxxxx    ?
>
> I executed the following lines several times from a script as well as
> pasting them in an R shell.
> Systematically biomaRt is failing.
> The problem is to extract the 3UTR sequences corresponding to a vector
> containing 1941
> Ensembl Transcript numbers (some are duplicated ... is this s problem ?)
> Please, find the failing instructions in the following including the ENST
> vector
>
> Any suggestion is welcome. Thank you,
> Maura
>
> > hmart <- useMart('ensembl', dataset='hsapiens_gene_ensembl')
> Checking attributes ... ok
> Checking filters ... ok
>
> > genes_map[,"ensembl_transcript_id"]
>   [1] "ENST00000262187" "ENST00000296271" "ENST00000346166"
> "ENST00000381570"
>
> <snip>
>
> [1937] "ENST00000400907" "ENST00000400908" "ENST00000440864"
> "ENST00000309042"
> [1941] "ENST00000254325"
>
> > genes_seq <- getSequence
> (id=genes_map[,"ensembl_transcript_id"],type="ensembl_transcript_id",
> + seqType="3utr",mart=hmart)
> Error in value[[3L]](cond) :
>  Request to BioMart web service failed. Verify if you are still connected
> to the internet.  Alternatively the BioMart web service is temporarily down.
>
>
>
> tutti i telefonini TIM!
>
>
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>
> tutti i telefonini TIM!
>
>
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