Hi Maura,

This also works for me and duplicate transcript ids shouldn't give problems,
you'll only get unique results back though.
What version of biomaRt are you running?
Would you be able to send me your complete transcript id list as an rda so I
can try the complete list?

Cheers,
Steffen

On Fri, May 28, 2010 at 1:54 PM, michael watson (IAH-C) <
michael.watson@bbsrc.ac.uk> wrote:

> 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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>
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