

-----Messaggio originale-----
Da: Steve Lianoglou [mailto:mailinglist.honeypot@gmail.com]
Inviato: ven 28/05/2010 17.06
A: mauede@alice.it
Cc: r-help@stat.math.ethz.ch
Oggetto: Re: [R] why biomaRt cannot extract 3UTR sequences for 1941 ENSGxxxxx ?
 
Hi,

Two things:

1. You mistakenly posted this to the R-help list, when you should have
(and probably meant to) send to the bioconductor list. You might want
to repost there if you can't figure out the problem.

   That's right. I apologize for my mistake. I will repost to the right list

2. I just tried your query with 4 transcript IDs (one of them was a
duplicate) and it worked fine.

Maybe the error you are receiving is actually informative of what your
problem is:

> 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.

and for some reason you're just having a problem talking to the
biomart service itself ...

Why not try your query with a small number of ensemble transcript id's
to see if that'll work?

  Actually, the same query has worked with a smaller number of ENST...many times.
  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



-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact




tutti i telefonini TIM!


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