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 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Wolfgang Raffelsberger, PhD Laboratoire de BioInformatique et G?nomique Int?grative IGBMC 1 rue Laurent Fries, 67404 Illkirch Strasbourg, France Tel (+33) 388 65 3300 Fax (+33) 388 65 3276 wolfgang.raffelsberger at igbmc.u-strasbg.fr

On Tuesday 23 January 2007 07:33, Wolfgang Raffelsberger wrote: > 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) ? Wolfgang, Give it a try and let us know how it works! You can probably make 200 copies of the same array with different filenames, if you want. Or download a bunch of .CEL files from NCBI GEO. Take a look at GSE2109, which has 1400 samples on the plus2 array, if I remember correctly. Sean

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 > > -- Aedi?n 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

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