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. 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

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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- 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

Hi Robert, Here is a traceback of the error I found. library(topGO) library(GOstats) BP.GOdataEG <- list(new("topGOdata", ontology = "BP", allGenes = geneListEG[[1]], + description = paste("GO BP analysis of 08.3.29 MCAT proteins",labs[1]), + 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 > traceback() 8: as.list.default(GOParents) 7: as.list(GOParents) 6: GO.getRoot(GOParents) 5: buildGOgraph.topology(mostSpecificGOs, ontology) 4: .local(.Object, ...) 3: initialize(value, ...) 2: initialize(value, ...) 1: new("topGOdata", ontology = "BP", allGenes = geneListEG[[1]], description = paste("GO BP analysis of 08.3.29 MCAT proteins", labs[1]), annot = annFUN.gene2GO, gene2GO = gene2GO) 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 RBGL_1.14.0 [6] annotate_1.16.0 xtable_1.5-1 GO.db_2.0.0 topGO_1.4.0 SparseM_0.73 [11] AnnotationDbi_1.0.6 RSQLite_0.6-3 DBI_0.2-3 GO_2.0.0 Biobase_1.16.0 [16] 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 ********************************************************************** ********* On Mon, 31 Mar 2008, Robert Gentleman wrote: > if you were to run traceback() right after the error, that would help us pin > point the actual code that was being evaluated... > > Dick Beyer wrote: >> 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 >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>> >>> -- >>> 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 >>> >> >> >> > > -- 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 >