-----Messaggio originale----- Da: Steve Lianoglou [mailto:mailinglist.honey...@gmail.com] Inviato: ven 28/05/2010 17.06 A: mau...@alice.it Cc: r-h...@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) : > Â Request to BioMart web service failed. Verify if you are still connected to > the internet. Â 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! [[alternative HTML version deleted]]
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