Hi, I am running R 2.0.1.1. on Windows. It is a Dell Dimension with a 3.2 Ghz Processor and 4Gb RAM. When using the ReadAffy() function to read in 97 arrays, I get the below error messages: Error: cannot allocate vector of size 393529 Reached total allocation of 1024Mb: see help(memory.size) When I use the comman "memory.limit(size=4000)" to increase the memory size to the maximum available, I got a "NULL" as a response. I proceeded to re-run ReadAffy(). This time, I only get the first error message. Error: cannot allocate vector of size 393529>From what I've read, this is more of a problem with Windows than with R. But I am wondering if there is anything I can do, either with the set up of R or Windows, to solve this problem and read the data set into R using this machine.Thank you for your attention, Christina
Christina Yau wrote:> Hi, > > I am running R 2.0.1.1. on Windows. It is a Dell Dimension with a > 3.2 Ghz Processor and 4Gb RAM.This question concerns a BioC package, so the correct listserv is bioconductor at stat.math.ethz.ch, not the R-help listserv. In the future, you should direct questions about BioC packages there. You don't have enough memory to read all 97 arrays into an AffyBatch, not to mention doing any further processing on them. You will have to use justRMA() or justGCRMA() to process your data. In addition, I don't think you can access any more than 2 Gb of RAM anyway without making some changes. See 2.11 of the Windows FAQ. HTH, Jim> > When using the ReadAffy() function to read in 97 arrays, I get the > below error messages: Error: cannot allocate vector of size 393529 > Reached total allocation of 1024Mb: see help(memory.size) > > When I use the comman "memory.limit(size=4000)" to increase the > memory size to the maximum available, I got a "NULL" as a response. > > I proceeded to re-run ReadAffy(). This time, I only get the first > error message. Error: cannot allocate vector of size 393529 > >> From what I've read, this is more of a problem with Windows than >> with R. But I am wondering if there is anything I can do, either >> with the set up of R or Windows, to solve this problem and read the >> data set into R using this machine. > > Thank you for your attention, Christina > > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the > posting guide! http://www.R-project.org/posting-guide.html-- James W. MacDonald University of Michigan Affymetrix and cDNA Microarray Core 1500 E Medical Center Drive Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
memory.limit may not be the correct command. I use the command 'utils:: memory.size(3*1024)' to increase my memory size after using editbin to modify the header of R to make it LARGEADDRESSAWARE as described in the above FAQ. I am able to read about 2.7Gb into memory that way with 4Gb of ram. Not only am I able to read it into memory, but I can do regessions on subsets of the data no problem. My question has always been, why can't R ship LARGEADDRESSAWARE for those users who may not have access to 'editbin' type tools? Thanks, Roger On 9/28/05, Christina Yau <cyau@buckinstitute.org> wrote:> > Hi, > > I am running R 2.0.1.1 <http://2.0.1.1>. on Windows. It is a Dell > Dimension with a 3.2 Ghz Processor and 4Gb RAM. > > When using the ReadAffy() function to read in 97 arrays, I get the below > error messages: > Error: cannot allocate vector of size 393529 > Reached total allocation of 1024Mb: see help(memory.size) > > When I use the comman "memory.limit(size=4000)" to increase the memory > size to the maximum available, I got a "NULL" as a response. > > I proceeded to re-run ReadAffy(). This time, I only get the first error > message. > Error: cannot allocate vector of size 393529 > > >From what I've read, this is more of a problem with Windows than with R. > But I am wondering if there is anything I can do, either with the set up of > R or Windows, to solve this problem and read the data set into R using this > machine. > > Thank you for your attention, > Christina > > ______________________________________________ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! > http://www.R-project.org/posting-guide.html >[[alternative HTML version deleted]]