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 ;-) Best, + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org

"Tony Chiang" <tchiang at="" fhcrc.org=""> writes: > Hi Naomi, > > Can you try this: > > source("http://www.bioconductor.org/biocLite.R")biocLite("GOstats") The formatting got messed up, so just to be clear you want: source("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. It is not one of the defaults. And in general, if you want a particular package, you should ask biocLite for it directly. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org

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 www.bioconductor.org and typed. source("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 <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 ;-) > >Best, > >+ seth > >-- >Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center >http://bioconductor.org > >_______________________________________________ >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 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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Specifically the change that I want to make is to allow duplicates. We are using novel species. Several genes from our species may hit the same gene from the closest model species due to duplication events since diversion. So, I need to allow duplicates in both the universe and the test set. I'll play with the code a bit - using weights might be the simplest. --Naomi 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 ;-) > >Best, > >+ seth > >-- >Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center >http://bioconductor.org > >_______________________________________________ >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 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