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. Thank you, Maura -----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! [[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 tutti i telefonini TIM! [[alternative HTML version deleted]]

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! > > > [[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 > > > > > tutti i telefonini TIM! > > > [[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]]