Dear BioC users, I would like to perform gene set analysis with gage analysis using the gene I previously selected as differentially expressed in my condition of interest. My first problem is that I am working with E. coli for which I couldn't find neither kegg.gs or go.gs like files. I thus wanted to create my own gene set collection using GSEABase and the following command lines where namesallexpr is the vectir of my 10208 probe identifier. I tried to use this with different computers but I always receive an error message (reported below) concerning memory problem. On my own labtop I also have an additional warning about a lack of virtual memory... Does anyone has tricks or suggestions to circumvent this memory problem? Unless it is a progarammation error? Does any one has already created such a gene collection (I am interested both in GO and KEGG collection) for ecoli2 affymetrix biochip and is ready to share it? Many thanks for your help, Cl?mentine > KEGGids=unique(mget(namesallexpr,ecoli2ENZYME,ifnotfound=NA)) > KEGGids=KEGGids[-1] > KEGGids=as.character(KEGGids[-1]) > > lst=as.list(ecoli2PATH) > gscKEGG = GeneSetCollection(mapply(function(geneIds,KEGGids) { + GeneSet(geneIds=namesallexpr, geneIdType=EntrezIdentifier(), + collectionType=KEGGCollection(KEGGids), + setName=KEGGids)}, lst, names(lst))) Erreur : impossible d'allouer un vecteur de taille 40 Ko De plus : Messages d'avis : 1: In names(object) <- NULL : Reached total allocation of 959Mb: see help(memory.size) 2: In initialize(value, ...) : Reached total allocation of 959Mb: see help(memory.size) 3: In initialize(value, ...) : Reached total allocation of 959Mb: see help(memory.size) 4: In initialize(value, ...) : Reached total allocation of 959Mb: see help(memory.size) > sessionInfo() R version 2.12.0 (2010-10-15) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252 LC_MONETARY=French_France.1252 [4] LC_NUMERIC=C LC_TIME=French_France.1252 attached base packages: [1] grid stats graphics grDevices utils datasets methods base other attached packages: [1] GSEABase_1.12.0 ecoli2cdf_2.6.0 XML_3.2-0.1 gage_2.0.0 multtest_2.6.0 [6] ecoli2.db_2.4.7 org.EcK12.eg.db_2.4.6 simpleaffy_2.26.0 gcrma_2.22.0 genefilter_1.32.0 [11] annotate_1.28.0 biomaRt_2.6.0 GOstats_2.16.0 graph_1.28.0 Category_2.16.0 [16] annaffy_1.22.0 KEGG.db_2.4.5 GO.db_2.4.5 RSQLite_0.9-2 DBI_0.2-5 [21] AnnotationDbi_1.12.0 lattice_0.19-13 affy_1.28.0 Biobase_2.10.0 limma_3.6.0 loaded via a namespace (and not attached): [1] affyio_1.18.0 Biostrings_2.18.0 IRanges_1.8.0 MASS_7.3-8 preprocessCore_1.12.0 [6] RBGL_1.25.1 RCurl_1.4-4.1 splines_2.12.0 survival_2.35-8 tools_2.12.0 [11] xtable_1.5-6 > -- Cl?mentine Dressaire Post-doctoral research fellow Control of gene expression lab ITQB - Instituto de Tecnologia Qu?mica e Biol?gica Apartado 127, Av. da Rep?blica 2780-157 Oeiras Portugal +351 214469562