This did not produce any error messages, but "Matrix" is still not 
available when I type

library(GOstats)

--Naomi

At 09:37 AM 5/1/2007, Tony Chiang wrote:
>Hi Naomi,
>
>Can you try this:
>
>source("<http://www.bioconductor.org/biocLite.R>http://www.bioconductor.org/biocLite.R")
>biocLite("GOstats")
>
>I have forgotten if GOstats if apart of the default packages that 
>biocLite automatically downloads, but from what you have written it 
>does not appear to be. Therefore, you actually have to tell biocLite 
>to get this particular package...and this should install all its 
>dependencies as well.
>
>Let us know if this still does not work for you.
>
>Tony
>
>
>
>
>
>On 5/1/07, Naomi Altman <<mailto:naomi@stat.psu.edu> 
>naomi@stat.psu.edu> wrote:
>source(" http://www.bioconductor.org/biocLite.R")
>Dear James and Seth,
>
>I downloaded the latest version of R yesterday.  I then followed the
>directions on <http://www.bioconductor.org>www.bioconductor.org and typed.
>
>source("<http://www.bioconductor.org/biocLite.R>http://www.bioconductor.org/biocLite.R")
>biocLite()
>
>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.
>
>--Naomi
>
>At 06:13 PM 4/30/2007, Seth Falcon wrote:
> >Naomi Altman <<mailto:naomi@stat.psu.edu>naomi@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 ;-)
> >
> >Best,
> >
> >+ seth
> >
> >--
> >Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
> ><http://bioconductor.org>http://bioconductor.org
> >
> >_______________________________________________
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> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>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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>https://stat.ethz.ch/mailman/listinfo/bioconductor
>Search the archives: 
><http://news.gmane.org/gmane.science.biology.informatics.conductor>http://news.gmane.org/gmane.science.biology.informatics.conductor
>

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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