Dear list,

I only need to compare GO terms associated with entrezID and
 I thought GOSim would be the easiest way to obtain one and only one GO 
ID (MF or BP) per entrezID. BiomaRt returns me many levels of GO annotation and I could not figure out how to keep, for example, MF level 2 only (i.e. I get 2442 GO from 642 genes, I want 642 max (some won't have any MF level 2 I think)).
My organism is Plasmodium. I also tried through the org.Pf.plasmo.db package too, but I don't think there is a way to select a specific GO level there.
In the end, I only need to generate 3 descriptive pie charts from 3 genelists of entrezID.

I'm trying to install GOSim, without success. I with the R under development version and R2.13.1 but it does not appear to be available in either of those version? Is it still supported and working or, most likely, am I making a mistake somewhere?

> source("http://www.bioconductor.org/biocLite.R")
BioC_mirror = http://bioconductor.org
Change using chooseBioCmirror().
Warning messages:
1: In safeSource() : Redefining ‘biocinstall’
2: In safeSource() : Redefining ‘biocinstallPkgGroups’
3: In safeSource() : Redefining ‘biocinstallRepos’
> biocLite("GOSim")
Using R version 2.13.1, biocinstall version 2.8.4.
Installing Bioconductor version 2.8 packages:
[1] "GOSim"
Please wait...

Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.13
Warning message:
In getDependencies(pkgs, dependencies, available, lib) :
  package ‘GOSim’ is not available (for R version 2.13.1)

> install.packages("GOSim", repos = "http://cran.r-project.org/web/packages/GOSim/", type="source")
Warning: unable to access index for repository http://cran.r-project.org/web/packages/GOSim/src/contrib
Warning message:
In getDependencies(pkgs, dependencies, available, lib) :
  package ‘GOSim’ is not available (for R version 2.13.1)
> sessionInfo()
R version 2.13.1 (2011-07-08)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] Biobase_2.12.2

loaded via a namespace (and not attached):
[1] tools_2.13.1
> 

Finally, I tried through the shell directly:

MacBook-Pro:~ apple$ R CMD INSTALL GOSim_1.2.5.tar.gz
* installing to library ‘/Library/Frameworks/R.framework/Versions/2.13/Resources/library’
ERROR: dependencies ‘topGO’, ‘flexmix’ are not available for package ‘GOSim’
* removing ‘/Library/Frameworks/R.framework/Versions/2.13/Resources/library/GOSim’
MacBook-Pro:~ apple$

Any suggestion?  
Thanks!

Olivier


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