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 [[alternative HTML version deleted]]