[BioC] biomaRt queries: optimal size?

[J.delasHeras at ed.ac.uk]

I've recently started to use biomaRt seriously. In teh past I just did  
a few tens of searches and all works fine. Now I have several datasets  
of several thousand IDs each.

I imagine that sending a single search with 3000 ids might not be a  
good idea. I tried, and it broke after a while... and got no results.

So I turned to divide the ids in blocks of 200, and proceeded to send  
my queries that way, 200 ids at a time, saving results as I go along.

This worked very well for my first set of 953 ids. When processing my  
secodn dataset of 1545 ids, the connection broke after 1200.

I obtained this error:
"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."

I am connected to the internet, and I see no evidence of Biomart being down...

Can this somehow be related to the size of my queries? I was trying to  
find what size is ok to send in one block, but I didn't find anything  
definite, only that sending one id at a time in a loop is not a good  
idea.

Any help greatly appreciated.

Thanks!

Jose

PS: sessionInfo()
R version 2.10.0 (2009-10-26)
i386-pc-mingw32

locale:
[1] LC_COLLATE=English_United Kingdom.1252
[2] LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] biomaRt_2.2.0

loaded via a namespace (and not attached):
[1] RCurl_1.2-1 XML_2.6-0


-- 
Dr. Jose I. de las Heras                      Email: J.delasHeras at ed.ac.uk
The Wellcome Trust Centre for Cell Biology    Phone: +44 (0)131 6513374
Institute for Cell & Molecular Biology        Fax:   +44 (0)131 6507360
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University of Edinburgh
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