Thanks Martin! The code worked and there were no problems importing the file. Regards Alice -----Original Message----- From: Martin Morgan [mailto:mtmorgan@fhcrc.org] Sent: Saturday, 7 June 2008 1:54 a.m. To: Johnstone, Alice Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] GSEA GeneSetCollection Hi Alice -- "Johnstone, Alice" <alice.johnstone at="" esr.cri.nz=""> writes: > Hi > I have been using the GSEA java version to look at my microarray > results. I ran into a problem as my samples are from rat. I > therefore want to create my own gene sets based on KEGG and GO > information in the annotation packages. I have used the command > gsc<-GeneSetCollection(Data,setType=KEGGCollection()) > to create a collection, which is fine, but I want to be able to use > this with the java version.. is it possible to create/export a gmx or > gmt file from R from the GeneSetCollection object? I don't think there's functionality available, but the following will create a gmt file, I think (untested beyond file creation) makeRow <- function(set) paste(setName(set), description(set), paste(geneIds(set), collapse="\t"), sep="\t") writeLines(sapply(gsc, makeRow), "/tmp/rats.gmt") Martin > Thanks > > Alice Johnstone > > PhD Student > Institute of Environmental Science and Research Ltd Kenepuru Science > Centre > 34 Kenepuru Drive > PO Box 50-348 > Porirua > New Zealand > > Tel: + 64 4 914-0717 > Fax: + 64 4 914-0770 > > > >> sessionInfo() > R version 2.7.0 (2008-04-22) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_New Zealand.1252;LC_CTYPE=English_New > Zealand.1252;LC_MONETARY=English_New > Zealand.1252;LC_NUMERIC=C;LC_TIME=English_New Zealand.1252 > > attached base packages: > [1] splines tools stats graphics grDevices utils datasets > methods base > > other attached packages: > [1] GSEABase_1.2.1 multtest_1.20.0 simpleaffy_2.16.0 > genefilter_1.20.0 > [5] survival_2.34-1 sma_0.5.15 rat2302probe_2.2.0 > rat2302cdf_2.2.0 > [9] MASS_7.2-41 gcrma_2.12.1 matchprobes_1.12.0 > illuminaRatBCv1_1.1.0 > [13] beadarray_1.8.0 affy_1.18.0 preprocessCore_1.2.0 > affyio_1.8.0 > [17] geneplotter_1.18.0 annotate_1.18.0 xtable_1.5-2 > lattice_0.17-6 > [21] limma_2.14.1 pcot2_1.8.0 amap_0.8-2 > rat2302.db_2.2.0 > [25] AnnotationDbi_1.2.0 RSQLite_0.6-8 DBI_0.2-4 > Biobase_2.0.1 > [29] rat2302_2.2.0 > > loaded via a namespace (and not attached): > [1] cluster_1.11.10 graph_1.18.0 grid_2.7.0 > KernSmooth_2.22-22 RColorBrewer_1.0-2 > [6] XML_1.93-2.1 > > P Think before you print > This e-mail transmission and any attachments that accompany it may contain information that is privileged, confidential or otherwise exempt from disclosure under applicable law and is intended solely for the use of the individual(s) to whom it was intended to be addressed. > If you have received this e-mail by mistake, or you are not the intended recipient, any disclosure, dissemination, distribution, copying or other use or retention of this communication or its substance is prohibited. If you have received this communication in error, please immediately reply to the author via e-mail that you received this message by mistake and also permanently delete the original and all copies of this e-mail and any attachments from your computer. Thank you. > > _______________________________________________ > 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 -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793