[BioC] Reading hundrets of .cel files and QC thereof

[Aedin Culhane]

Dear Wolfgang
You definitely will have problems reading 200 cel files.  I use a 32 RAM 
machine that falls in my fitPLM script when I have over 300 cel files. 
It falls over at ReadAffy. I was thinking of affxparser instead.  Maybe 
try this. If it works let me know ;-)
Thanks
Aedin


> Date: Tue, 23 Jan 2007 13:33:34 +0100
> From: Wolfgang Raffelsberger <wraff at titus.u-strasbg.fr>
> Subject: [BioC] Reading hundrets of .cel files and QC thereof
> To: bioconductor at stat.math.ethz.ch
> Message-ID: <45B6009E.3010202 at igbmc.u-strasbg.fr>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> Dear Bioconductors,
> 
> I'm preparing for two projects with 200 arrays each (U133+2).
> Currently I use a Fedora (Core 5) Linux Quad AMD Opteron at 16 Go RAM.
> Reading a recent post on this list I guess reading the cel files using 
> justRMA() or justGCRMA() won't be the probelm.
> But does have anyone experience if this is sufficient (or how much I'd 
> need) to run QC based on fitPLM(), RLE & NUSE or the affyQCReport package ?
> Do you have other suggestions for running QC (besides chopping the 
> projects in smaller chunks) ?
> 
>  > sessionInfo()
> R version 2.4.1 (2006-12-18)
> x86_64-unknown-linux-gnu
> 
> Thank's in advance,
> Wolfgang
> 
>  



-- 
Aedi­n Culhane,
Research Associate in Prof. J Quackenbush Lab
Harvard School of Public Health, Dana-Farber Cancer Institute

44 Binney Street, SM822
Department of Biostatistics and Computational Biology,
Dana-Farber Cancer Institute
Boston, MA 02115
USA

Phone: +1 (617) 632 2468
Fax:   +1 (617) 582 7760
Email: aedin at jimmy.harvard.edu
Web URL: http://www.hsph.harvard.edu/researchers/aculhane.html