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Hi Ingrid, Ingrid H. G. ?stensen wrote: > Hi > > I have found GO categorys in a data set and want to see which genes are in the different terms that are listed. Previously I have done the following: > > annoPk <- "illuminaHumanv2" > entrezPk <- illuminaHumanv2ENTREZID > pVerdi_GO = 0.01 > > probe <- top2[,1] #top2 is a topTable object > > sigLL <- (unlist(mget(probe, env=entrezPk, ifnotfound=NA))) > sigLL <- sigLL[!is.na(sigLL)] > sigLL <- sigLL[!duplicated(sigLL)] > > univ <- unique(getLL(ls(entrezPk), annoPk)) > > > params <- new("GOHyperGParams", geneIds= sigLL, universeGeneIds=univ, annotation=annoPk, ontology="BP", pvalueCutoff= pVerdi_GO, conditional=TRUE, testDirection="over") > hgOver <- hyperGTest(params) > res_filNavn <- paste(i, "_GO_summary_BP_over.html", sep = "") > htmlReport(hgOver,file=res_filNavn) > ps <- probeSetSummary(hgOver) > res_filNavn_gener <- paste(i, "_GO_prober_BP_over.txt") > for(j in 1:length(ps)) > { > write.table(ps[j], file = res_filNavn_gener, append=TRUE, sep="") > } > > This has worked fine. But now I am reading the topTable result as an .txt file (topTable files made previously and stored as a .txt file). I now have to use as.character to get the information into hyperGTest. > > sigLL <- (unlist(mget(as.character(probe), env=entrezPk, ifnotfound=NA))) > sigLL <- as.character(sigLL[!is.na(sigLL)]) > sigLL <- sigLL[!duplicated(sigLL)] > > univ <- as.character(unique(getLL(ls(entrezPk), annoPk))) > > Unfortenatly probeSetSummary does not like this: > > >> ps <- probeSetSummary(hgOver) > Warning message: > The vector of geneIds used to create the GOHyperGParams object was not a named vector. > If you want to know the probesets that contributed to this result > you need to pass a named vector for geneIds. > > Is it possible to read a .txt file and get the probe ID into a named vector? Or get around this another way? I have tried on R 2.5.1 and 2.6. Sure. Just read in the .txt file and then create another vector of names for the vector, and do names(thevector) <- thenamevector Of course this presupposes that you know the names for the vector... If not, I think you are stuck. Best, Jim > >> sessionInfo() > R version 2.6.0 (2007-10-03) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United Kingdom.1252;LC_MONETARY=English_United Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 > > attached base packages: > [1] splines tools stats graphics grDevices utils datasets methods base > > other attached packages: > [1] illuminaHumanv2_1.4.0 GOstats_2.4.0 Category_2.4.0 genefilter_1.16.0 survival_2.34 RBGL_1.14.0 GO.db_2.0.2 graph_1.16.1 > [9] lumi_1.4.0 mgcv_1.3-28 affy_1.16.0 preprocessCore_1.0.0 affyio_1.6.1 annaffy_1.10.1 KEGG_2.0.1 GO_2.0.1 > [17] annotate_1.16.1 AnnotationDbi_1.0.6 RSQLite_0.6-4 DBI_0.2-4 Biobase_1.16.1 xtable_1.5-2 RColorBrewer_1.0-2 limma_2.12.0 > > loaded via a namespace (and not attached): > [1] cluster_1.11.9 > > Regards, > Ingrid > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623

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