just.RMA works. Thanks. >>> Martin Morgan <mtmorgan@fhcrc.org> 3/30/2011 11:50 AM >>> On 03/30/2011 07:58 AM, Steve Lianoglou wrote: > Hi, > > On Wed, Mar 30, 2011 at 10:35 AM, Xiaobin Yuan > <xiaobin.yuan@louisville.edu> wrote: >> Dear list, >> >> My colleague can not read some cel files. There 24 CEL files. Each >> file has the size of 13M. The following is the error message: >> >> data<-ReadAffy() >> Error: cannot allocate vector of size 248.1 Mb >> >> If only put 12 files in the directory, R can read it without error. >> Does anyone has this problem before? >> >> Those files can be read in my computer. And the size of RAM is the >> same for our computers. > > Somehow your colleague has access to less of the RAM than you do ... > is he running other programs? Is he running R in 32 bit mode? > > Another thing to consider is looking at the aroma-project if you have > more microarrays than your cpu does RAM: > http://www.aroma-project.org/ The functions just.rma in affy, just.gcrma (gcrma) are more memory efficient implementations for the common work flow from CEL to ExpressionSet via RMA / GCRMA. Martin > > -steve > -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793 [[alternative HTML version deleted]]

Hi, I already get that problem under windows. There a function to increase memory that windows can use. I put it with an if to detect the OS so it don't cause any error if you run it under linux or windows because the function to allocate memory only work under windows. So now, every R script I create automatically contain those line. #Allocate memory under windows if (.Platform$OS.type == "windows") { memory.limit(size = 4095) memory.limit() } Simon No?l CdeC ________________________________________ De : bioconductor-bounces at r-project.org [bioconductor-bounces at r-project.org] de la part de Lenka Radova [avodar at gmail.com] Date d'envoi : 30 mars 2011 14:29 ? : bioconductor at r-project.org Objet : Re: [BioC] memory problem to read CEL files Hi, try data <- justRMA() it will give you the same final data as data1<- ReadAffy() data<-rma(data1) Lenka 2011/3/30, Steve Lianoglou <mailinglist.honeypot at="" gmail.com="">: > Hi, > > On Wed, Mar 30, 2011 at 10:35 AM, Xiaobin Yuan > <xiaobin.yuan at="" louisville.edu=""> wrote: >> Dear list, >> >> My colleague can not read some cel files. There 24 CEL files. Each >> file has the size of 13M. The following is the error message: >> >> data<-ReadAffy() >> Error: cannot allocate vector of size 248.1 Mb >> >> If only put 12 files in the directory, R can read it without error. >> Does anyone has this problem before? >> >> Those files can be read in my computer. And the size of RAM is the >> same for our computers. > > Somehow your colleague has access to less of the RAM than you do ... > is he running other programs? Is he running R in 32 bit mode? > > Another thing to consider is looking at the aroma-project if you have > more microarrays than your cpu does RAM: > http://www.aroma-project.org/ > > -steve > > -- > Steve Lianoglou > Graduate Student: Computational Systems Biology > | Memorial Sloan-Kettering Cancer Center > | Weill Medical College of Cornell University > Contact Info: http://cbio.mskcc.org/~lianos/contact > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor