Hi I have tried to run different QC operation on 36 .cel files of the type U-133+2 using different Linux servers. On the 32 bits system (8 Mb RAM) it did not go very well for all the QC operations, but on a 62 bit system things went fine. (I do not know how much RAM was on the 64 bit system.) So if you have access to a 64 bit system, us it. Regards, Ingrid -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch on behalf of Aedin Culhane Sent: Wed 1/24/2007 12:34 To: bioconductor@stat.math.ethz.ch Subject: Re: [BioC] Reading hundrets of .cel files and QC thereof 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 > Subject: [BioC] Reading hundrets of .cel files and QC thereof > To: bioconductor@stat.math.ethz.ch > Message-ID: <45B6009E.3010202@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@jimmy.harvard.edu Web URL: http://www.hsph.harvard.edu/researchers/aculhane.html _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]