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Hi Naomi, Naomi Altman wrote: > I am having some problems with hyperGTest. See below. Also, I > wanted to modify hyperGTest for my project, but I cannot seem to find > any relevant code. There must be some secret to names for functions > for this type of thing - please point me in the right direction. > > The relevant bits for the error are (I hope) below: > > > R version 2.5.0 (2007-04-23) > Copyright (C) 2007 The R Foundation for Statistical Computing > ISBN 3-900051-07-0 > > ,,, > > > > > library(GOstats) > Loading required package: graph > Loading required package: Biobase > Loading required package: tools > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation(pkgname)'. > > Loading required package: GO > Loading required package: annotate > Loading required package: RBGL > Loading required package: Category > Loading required package: KEGG > Loading required package: genefilter > Loading required package: survival > Loading required package: splines > Loading required package: Matrix > Error: package 'Matrix' could not be loaded ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ You are missing the Matrix package, so GOstats never loaded. Best, Jim > In addition: Warning message: > there is no package called 'Matrix' in: library(pkg, character.only = > TRUE, logical = TRUE, lib.loc = lib.loc) > > > paramsBPI=new("GOHyperGParams",geneIds=clustI,universeGeneIds=refs, > + annotation="ath1121501", > ontology="BP",pvalueCutoff=0.05,conditional=FALSE, testDirection="over") > Error in getClass(Class, where = topenv(parent.frame())) : > "GOHyperGParams" is not a defined class > > hgBPI=hyperGTest(paramsBPI) > Error: could not find function "hyperGTest" > > > Naomi S. Altman 814-865-3791 (voice) > Associate Professor > Dept. of Statistics 814-863-7114 (fax) > Penn State University 814-865-1348 (Statistics) > University Park, PA 16802-2111 > > [[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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.