R help - Apr 2009 - DNAcopy package in R

Hi All:

Has anyone analyzed Illumina 550K data using DNAcopy package? I have around
2300 samples. According to
Venkatraman and Olshen 2007 paper, it needs about 25 min to run a single
sample for Affymetrix 100K. I am afraid it will take too long to analyzed my
data. Anybody has an idea? Thanks!

Best, 
-- 
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Probably better asked on the BioC list.

On Apr 21, 2009, at 11:40 AM, Selena Niu wrote:
> Has anyone analyzed Illumina 550K data using DNAcopy package? I have  
> around
> 2300 samples. According to
> Venkatraman and Olshen 2007 paper, it needs about 25 min to run a  
> single
> sample for Affymetrix 100K. I am afraid it will take too long to  
> analyzed my
> data. Anybody has an idea? Thanks!
David Winsemius, MD
Heritage Laboratories
West Hartford, CT

Dear Selena,

You probably will want to try to run this in a computing cluster,
parallelizing over samples.

Best,

R.

On Tue, Apr 21, 2009 at 5:40 PM, Selena Niu <yue.niu at yale.edu>
wrote:
>
> Hi All:
>
> Has anyone analyzed Illumina 550K data using DNAcopy package? I have around
> 2300 samples. According to
> Venkatraman and Olshen 2007 paper, it needs about 25 min to run a single
> sample for Affymetrix 100K. I am afraid it will take too long to analyzed
my
> data. Anybody has an idea? Thanks!
>
> Best,
> --
> View this message in context:
http://www.nabble.com/DNAcopy-package-in-R-tp23158907p23158907.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
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> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>


-- 
Ramon Diaz-Uriarte
Statistical Computing Team
Structural Biology and Biocomputing Programme
Spanish National Cancer Centre (CNIO)
http://ligarto.org/rdiaz
Phone: +34-91-732-8000 ext. 3019