Dear Jim, Thank you so much for the explanation. I will bear your suggestions in my mind and will plan my analysis accordingly. Thanks, kishor On Thu, Sep 17, 2009 at 6:45 PM, James W. MacDonald <jmacedon at="" med.umich.edu=""> wrote: > Hi Kishor, > > Kishor Tappita wrote: >> >> Dear List, >> >> I am trying to use gene2pathway package for finding enriched pathways. >> When I try to retrain the >> model of homo sapiens I get the below error. It works fine for drosophila. >> >>> retrain(KEGG.package=TRUE, organism="hsa") >> >> Retrieving KEGG information via KEGG.db package ... >> done >> Retrieving information from InterPro database for organism ' hsa ' via >> Ensembl ... >> Checking attributes ... ok >> Checking filters ... ok >> Error: cannot allocate vector of size 248.4 Mb > > This means that you are running out of RAM. You might or might not be able > to get around this problem, depending on your current configuration. There > are some things you can try: > > If you have less than 4 Gb RAM, you could add more. > > If this occurred in an R session where you had lots of other objects loaded, > you could try again with a new R session, making sure you don't load > extraneous objects (or remove things you don't need and ensure recapture of > memory using gc()). > > Note that recapturing memory on Windows isn't as effective as on other > operating systems, as Windows isn't good at handling memory and usually > requires contiguous space for large objects. > > If you have access to a computer or server with more memory, that would be > the easiest fix. > > Best, > > Jim > > >> >>> sessionInfo() >> >> R version 2.9.2 (2009-08-24) >> i386-pc-mingw32 >> >> locale: >> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >> States.1252;LC_MONETARY=English_United >> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >> >> attached base packages: >> [1] grid ? ? ?stats ? ? graphics ?grDevices utils ? ? datasets ?methods >> [8] base >> >> other attached packages: >> ?[1] gene2pathway_1.2.0 ? ?org.Dm.eg.db_2.2.11 ? RBGL_1.20.0 >> ?[4] KEGGSOAP_1.18.0 ? ? ? KEGG.db_2.2.11 ? ? ? ?kernlab_0.9-8 >> ?[7] Rgraphviz_1.22.1 ? ? ?hgu133plus2.db_2.2.11 topGO_1.12.0 >> [10] SparseM_0.80 ? ? ? ? ?graph_1.22.2 ? ? ? ? ?GO.db_2.2.11 >> [13] RSQLite_0.7-2 ? ? ? ? DBI_0.2-4 ? ? ? ? ? ? AnnotationDbi_1.6.1 >> [16] limma_2.18.3 ? ? ? ? ?GEOquery_2.8.0 ? ? ? ?RCurl_0.98-1 >> [19] bitops_1.0-4.1 ? ? ? ?Biobase_2.4.1 ? ? ? ? biomaRt_2.0.0 >> >> loaded via a namespace (and not attached): >> [1] lattice_0.17-25 SSOAP_0.4-6 ? ? tools_2.9.2 ? ? XML_2.5-1 >> >> Please help me overcome this problem. >> >> Thanks, >> Kishor >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- > James W. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 >