Hi, I have a problem to understand what I type of variables I have to feed into the function vennSelect. As the vennDiagram is only able to get the overlap between multiple contrasts depending on the p.value (btw: can I use the decideTests function dependent on the adj.p.value, too?), I took a look at the vennSelect function which appears to be made for extactly this case. What I did: a <- ReadAffy(filenames = rownames(pData(pd)), phenoData = pd, verbose = TRUE) x <- expresso(a, bg.correct = FALSE, normalize.method = "vsn", normalize.param = list(subsample = 1000), pmcorrect.method = "pmonly", summary.method = "medianpolish") design <- model.matrix(~ -1+factor(c(1,1,1,2,2,2,3,3,3))) colnames(design) <- c("control", "four", "sixteen") fit <- lmFit(x, design) contrast.matrix <- makeContrasts(four-control, sixteen-control, levels=design) fit2 <- contrasts.fit(fit, contrast.matrix) fit2 <- eBayes(fit2) results <- decideTests(fit2) Now I try: vennSelect(x,design,results,contrast.matrix,fit2) but I get: Loading required package: hgu133plus2 Error in aaf.handler(chip = chip) : Couldn't load data package hgu133plus2 In addition: Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called 'hgu133plus2' unfortunately it seems I cannot install hgu133plus2: biocLite("hgu133plus2") Running biocinstall version 2.3.14 with R version 2.8.1 Your version of R requires version 2.3 of Bioconductor. Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : argument 'lib' is missing: using '/Users/maxim/Library/R/2.8/library' Warning message: package ‘hgu133plus2’ is not available What is wrong? Maxim sessionInfo() R version 2.8.1 (2008-12-22) i386-apple-darwin8.11.1 locale: en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] splines tools stats graphics grDevices utils datasets methods base other attached packages: [1] affycoretools_1.14.1 annaffy_1.14.0 KEGG.db_2.2.5 gcrma_2.14.1 matchprobes_1.14.1 [6] biomaRt_1.16.0 GOstats_2.8.0 Category_2.8.4 genefilter_1.22.0 survival_2.34-1 [11] RBGL_1.18.0 annotate_1.20.1 xtable_1.5-4 GO.db_2.2.5 graph_1.20.0 [16] hgu133plus2cdf_2.3.0 hgu133plus2.db_2.2.5 RSQLite_0.7-1 DBI_0.2-4 AnnotationDbi_1.4.2 [21] gplots_2.6.0 gdata_2.4.2 gtools_2.5.0-1 vsn_3.8.0 lattice_0.17-17 [26] limma_2.16.5 affy_1.20.2 Biobase_2.2.1 loaded via a namespace (and not attached): [1] GSEABase_1.4.0 RCurl_0.94-1 XML_2.3-0 affyio_1.10.1 cluster_1.11.11 [6] grid_2.8.1 preprocessCore_1.4.0 [[alternative HTML version deleted]]

Hi Maxim, You want an annotation package, which for a few years now have a .db appended to the name. So try biocLite("hgu133plus2.db") and then re-run your analysis. Best, Jim Maxim wrote: > Hi, > > > I have a problem to understand what I type of variables I have to feed into > the function vennSelect. As the vennDiagram is only able to get the overlap > between multiple contrasts depending on the p.value (btw: can I use the > decideTests function dependent on the adj.p.value, too?), I took a look at > the vennSelect function which appears to be made for extactly this case. > What I did: > > > > a <- ReadAffy(filenames = rownames(pData(pd)), phenoData = pd, verbose = > TRUE) > > x <- expresso(a, bg.correct = FALSE, normalize.method = "vsn", > normalize.param > > = list(subsample = 1000), pmcorrect.method = "pmonly", summary.method = > > "medianpolish") > > > design <- model.matrix(~ -1+factor(c(1,1,1,2,2,2,3,3,3))) > > colnames(design) <- c("control", "four", "sixteen") > > fit <- lmFit(x, design) > > > contrast.matrix <- makeContrasts(four-control, sixteen-control, > levels=design) > > > fit2 <- contrasts.fit(fit, contrast.matrix) > > fit2 <- eBayes(fit2) > > > results <- decideTests(fit2) > > > Now I try: > > vennSelect(x,design,results,contrast.matrix,fit2) > > > but I get: > > > Loading required package: hgu133plus2 > > Error in aaf.handler(chip = chip) : > > Couldn't load data package hgu133plus2 > > In addition: Warning message: > > In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return > = TRUE, : > > there is no package called 'hgu133plus2' > > > unfortunately it seems I cannot install hgu133plus2: > > biocLite("hgu133plus2") > > Running biocinstall version 2.3.14 with R version 2.8.1 > > Your version of R requires version 2.3 of Bioconductor. > > Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = > dependencies, : > > argument 'lib' is missing: using '/Users/maxim/Library/R/2.8/library' > > Warning message: > > package ?hgu133plus2? is not available > > > What is wrong? > > > Maxim > > > > sessionInfo() > > R version 2.8.1 (2008-12-22) > > i386-apple-darwin8.11.1 > > > locale: > > en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > > attached base packages: > > [1] splines tools stats graphics grDevices utils datasets > methods base > > > other attached packages: > > [1] affycoretools_1.14.1 annaffy_1.14.0 KEGG.db_2.2.5 > gcrma_2.14.1 matchprobes_1.14.1 > > [6] biomaRt_1.16.0 GOstats_2.8.0 Category_2.8.4 > genefilter_1.22.0 survival_2.34-1 > > [11] RBGL_1.18.0 annotate_1.20.1 xtable_1.5-4 > GO.db_2.2.5 graph_1.20.0 > > [16] hgu133plus2cdf_2.3.0 hgu133plus2.db_2.2.5 RSQLite_0.7-1 > DBI_0.2-4 AnnotationDbi_1.4.2 > > [21] gplots_2.6.0 gdata_2.4.2 gtools_2.5.0-1 > vsn_3.8.0 lattice_0.17-17 > > [26] limma_2.16.5 affy_1.20.2 Biobase_2.2.1 > > > loaded via a namespace (and not attached): > > [1] GSEABase_1.4.0 RCurl_0.94-1 XML_2.3-0 > affyio_1.10.1 cluster_1.11.11 > > [6] grid_2.8.1 preprocessCore_1.4.0 > > [[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 Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues