Hi Olivier,

I worry that you might be confused about how GO annotations work.  Many 
genes will also be associated with multiple different terms, even from 
within the same ontology.  The only limit to how many terms can be used 
to describe a gene is how many of them actually apply, and many genes 
can have more than one kind of function or location in a cell.  So even 
if you restricted down to just one level of the tree, you still could 
have more than one GO term associated with a given gene.  Also, for the 
org packages at least the terms that will be in the standard GO mapping 
should be the ones that are the most appropriate for describing that 
gene.  That is unless you use the "GO2ALL" mapping, you should not get 
all of the DAG levels for each gene.

I hope this helps.  Please let me know if I have misunderstood you,

   Marc




On 08/29/2011 04:26 PM, Olivier Lucas wrote:
> 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 âEUR~biocinstallâEUR^(TM)
> 2: In safeSource() : Redefining âEUR~biocinstallPkgGroupsâEUR^(TM)
> 3: In safeSource() : Redefining âEUR~biocinstallReposâEUR^(TM)
>> 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) :
> Â  package âEUR~GOSimâEUR^(TM) 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) :
> Â  package âEUR~GOSimâEUR^(TM) 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] statsÂ Â Â Â  graphicsÂ  grDevices utilsÂ Â Â Â  datasetsÂ  methodsÂ Â  baseÂ Â Â Â 
>
> 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 âEUR~/Library/Frameworks/R.framework/Versions/2.13/Resources/libraryâEUR^(TM)
> ERROR: dependencies âEUR~topGOâEUR^(TM), âEUR~flexmixâEUR^(TM) are not available for package âEUR~GOSimâEUR^(TM)
> * removing âEUR~/Library/Frameworks/R.framework/Versions/2.13/Resources/library/GOSimâEUR^(TM)
> MacBook-Pro:~ apple$
>
> Any suggestion?Â 
> Thanks!
>
> Olivier
>
>
> 	[[alternative HTML version deleted]]
>
>
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor


	[[alternative HTML version deleted]]

