error with "retrain" method of gene2pathway package
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@kishor-tappita-2563
Last seen 8.1 years ago
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 > 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
Pathways GO Organism Homo sapiens hgu133plus2 gene2pathway Pathways GO Organism • 773 views
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@james-w-macdonald-5106
Last seen 1 day ago
United States
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
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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 >
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