Hi, I'm trying to summarize the results of 47 cel files with the following command: allMtb.eset.liwong <- expresso(allMtb, normalize.method= "invariantset", bg.correct= FALSE, pmcorrect.method= "pmonly", summary.method= "liwong") Here is the progress report: normalization: invariantset PM/MM correction : pmonly expression values: liwong normalizing...Error: cannot allocate vector of size 360.0 Mb My sessionInfo: R version 2.11.1 (2010-05-31) i386-apple-darwin9.8.0 locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] mouse4302cdf_2.6.0 affy_1.26.1 Biobase_2.8.0 loaded via a namespace (and not attached): [1] affyio_1.16.0 preprocessCore_1.10.0 tools_2.11.1 Any thoughts on how I can get around the error? Thanks, Anjan -- =================================== anjan purkayastha, phd. research associate fas center for systems biology, harvard university 52 oxford street cambridge ma 02138 phone-703.740.6939 =================================== [[alternative HTML version deleted]]

Anjan you can either use a computer with more memory or use one of the several alternatives to 'expresso' that are more memory-efficient and have been discussed on this list so many times already (e.g. affy:rma or the xps package). Best wishes Wolfgang Il Oct/7/10 6:32 PM, ANJAN PURKAYASTHA ha scritto: > Hi, > I'm trying to summarize the results of 47 cel files with the following > command: > allMtb.eset.liwong<- expresso(allMtb, normalize.method= "invariantset", > bg.correct= FALSE, pmcorrect.method= "pmonly", summary.method= "liwong") > Here is the progress report: > normalization: invariantset > PM/MM correction : pmonly > expression values: liwong > normalizing...Error: cannot allocate vector of size 360.0 Mb > > My sessionInfo: > R version 2.11.1 (2010-05-31) > i386-apple-darwin9.8.0 > > locale: > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] mouse4302cdf_2.6.0 affy_1.26.1 Biobase_2.8.0 > > loaded via a namespace (and not attached): > [1] affyio_1.16.0 preprocessCore_1.10.0 tools_2.11.1 > > Any thoughts on how I can get around the error? > Thanks, > Anjan >