[R] why biomaRt cannot extract 3UTR sequences for 1941 ENSGxxxxx ?

Steve Lianoglou mailinglist.honeypot at gmail.com
Fri May 28 17:06:56 CEST 2010


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.

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?


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

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