[BioC] hyperGTest

Naomi Altman naomi at stat.psu.edu
Tue May 1 15:32:21 CEST 2007

Dear James and Seth,

I downloaded the latest version of R yesterday.  I then followed the 
directions on www.bioconductor.org and typed.


This did not install GOstats, so I pulled down the install packages 
menu and selected GOstats and gotools.

Since Matrix was not installed, I looked for it in bioconductor and 
CRAN and did not find it.  help.search did not reveal any clues.

I guess the problem now is to find the missing "Matrix" 
package.  Please advise.


At 06:13 PM 4/30/2007, Seth Falcon wrote:
>Naomi Altman <naomi at stat.psu.edu> writes:
> > 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.
>As Jim pointed out, you need the Matrix package.  This should have
>come along with an install of GOstats via biocLite(), but perhaps you
>installed using another mechanism.
>As for modifying the code for your project, you will want to download
>and unpack the source packages (.tar.gz) for Category and GOstats.
>The code is split between these packages since much of the
>Hypergeometric testing is not GO specific.
>There are a few notes in the man page for hyperGTest for how to extend
>to other category types if that is what you want to do.
>Given that you didn't have GOstats properly loaded, I imagine all of
>its functions would be rather invisible ;-)
>+ seth
>Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>Search the archives: 

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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