Hi, I d like to compare results obtained with different approaches with a set of 9 HU133A chips. One of these would be to use the rma background correction method and the invariant set normalization method but it seems that with ONLY 9 chips I am running out of memory !!! I have 1 Go RAM on XP Pro R1.7.1 and RMA 1.3.6... and nothing is running aside this program. I was expecting it to run under these conditions !!! Philippe > library(affy) > data<- ReadAffy() > data2<-expresso(data, bgcorrect.method="rma", normalize.method="invariantset", pmcorrect.method="pmonly", summary.method="medianpolish") background correction: rma normalization: invariantset PM/MM correction : pmonly expression values: medianpolish background correcting...Error: cannot allocate vector of size 35644 Kb [[alternative HTML version deleted]]

You probably need to add --max-mem-size=1G after RGui.exe in the target field of your R shortcut. Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> <phguardiol@aol.com> 08/09/03 06:46AM >>> Hi, I d like to compare results obtained with different approaches with a set of 9 HU133A chips. One of these would be to use the rma background correction method and the invariant set normalization method but it seems that with ONLY 9 chips I am running out of memory !!! I have 1 Go RAM on XP Pro R1.7.1 and RMA 1.3.6... and nothing is running aside this program. I was expecting it to run under these conditions !!! Philippe > library(affy) > data<- ReadAffy() > data2<-expresso(data, bgcorrect.method="rma", normalize.method="invariantset", pmcorrect.method="pmonly", summary.method="medianpolish") background correction: rma normalization: invariantset PM/MM correction : pmonly expression values: medianpolish background correcting...Error: cannot allocate vector of size 35644 Kb [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor