[BioC] topGO and GOstats conflict

[Dick Beyer]

Hi Robert,

I re-ran my code to see the error message when I load GOstats after topGO.

> 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))
+ }

Building most specific GOs .....        ( 3337 GO terms found. )

Build GO DAG topology ..........Error in as.vector(x, "list") : cannot coerce to vector

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] splines   tools     stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
  [1] GOstats_2.4.0       Category_2.4.0      genefilter_1.16.0   survival_2.34
  [5] RBGL_1.14.0         annotate_1.16.0     xtable_1.5-1        GO.db_2.0.0
  [9] topGO_1.4.0         SparseM_0.73        AnnotationDbi_1.0.6 RSQLite_0.6-3      
[13] DBI_0.2-3           GO_2.0.0            Biobase_1.16.0      graph_1.16.1

loaded via a namespace (and not attached):
[1] cluster_1.11.9


If I restart my R session and load GOstats then topGO, the above code works fine.  So you were right about this being a possible NAMESPACE issue.

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
*******************************************************************************

On Sun, 30 Mar 2008, Robert Gentleman wrote:

> 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.
>
> thanks
>  Robert
>
>
>> 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
> 206-667-7700
> rgentlem at fhcrc.org
>