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
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

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