[BioC] topGO and GOstats conflict

Dick Beyer dbeyer at u.washington.edu
Mon Mar 31 06:08:06 CEST 2008

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.

R version 2.6.1 (2007-11-26) 

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

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

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