[BioC] topGO and GOstats conflict

Robert Gentleman rgentlem at fhcrc.org
Mon Mar 31 06:27:52 CEST 2008

Thanks for the note Dick

Dick Beyer wrote:
> Just a note for people to find when they search the mail about a conflict between topGO and GOstats.
> I was running topGO successfully, then I loaded GOstats so I could plot some DAGs via GOGraph.  That worked just fine.  I then tried to rerun some topGO code and was unable to execute soemthing like this:
> BP.GOdataEG <- list() 
> for(i in 1:5){
>    BP.GOdataEG[i] <- list(new("topGOdata", ontology = "BP", allGenes = geneListEG[[i]],
>    description = paste("GO BP analysis of 08.3.29 MCAT proteins",labs[i]),
>    annot = annFUN.gene2GO, gene2GO = gene2GO))
> }
> I would get the message of "Building most specific GOs, but then I'd get an error on the "Build GO DAG topology" step saying something like couldn't make a vector from a list.  A bit obscure to me.  I haven't read the fine print on topGO or GOstats, so maybe having both packages loaded at the same time is forbidden.  Anyway, the fix is easy, just run one or the other.

that suggests that topGO is not using a NAMESPACE (Adrian, your package 
would likely benefit from having one, so that you have better control 
over which functions are getting picked up). The purpose of NAMESPACEs 
is to ensure that this does not happen.  I suspect, but am not sure that 
if you load GOstats first, then topGO that you would not have trouble. 
If you have the energy to try that and report back (but with the error, 
if there is one, not a summary) that could help.


> sessionInfo()
> R version 2.6.1 (2007-11-26) 
> i386-pc-mingw32
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets  methods   base
> other attached packages:
> [1] topGO_1.4.0         SparseM_0.73        AnnotationDbi_1.0.6 RSQLite_0.6-3       DBI_0.2-3          
> [6] GO_2.0.0            Biobase_1.16.0      graph_1.16.1
> loaded via a namespace (and not attached):
> [1] cluster_1.11.9
> Cheers,
> Dick
> *******************************************************************************
> Richard P. Beyer, Ph.D.	University of Washington
> Tel.:(206) 616 7378	Env. & Occ. Health Sci. , Box 354695
> Fax: (206) 685 4696	4225 Roosevelt Way NE, # 100
>  			Seattle, WA 98105-6099
> http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html
> http://staff.washington.edu/~dbeyer
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Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
rgentlem at fhcrc.org

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