[BioC] hyperGTest

[James W. MacDonald]

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]]
> 
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-- 
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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