Hi, I have a new problem with R code that worked under R2.8.1. When I run in my code (too long to reproduce): summary(hyperGTestresult) I get the error: Error in if (nrow(df) == 0) { : argument is of length zero Here's the result of: >hyperGTestresult Gene to GO BP test for over-representation 1824 GO BP ids tested (149 have p < 0.001) Selected gene set size: 252 Gene universe size: 12474 Annotation package: hgu133plus2 So it looks like the hyperGTest worked and found some significant terms. I can even extract the GO terms using sigCategories() and the pvalues using pvalues() but the summary() and htmlReport() methods return the same error. I did not have this problem using the same code in R2.8.1. >sessionInfo() R version 2.9.0 (2009-04-17) 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] stats graphics grDevices datasets utils methods base other attached packages: [1] GOstats_2.9.4 graph_1.21.7 Category_2.9.14 [4] annaffy_1.15.0 KEGG.db_2.2.11 GO.db_2.2.11 [7] hgu133plus2.db_2.2.11 RSQLite_0.7-1 DBI_0.2-4 [10] AnnotationDbi_1.5.23 RColorBrewer_1.0-2 gplots_2.6.0 [13] gdata_2.4.2 gtools_2.5.0-1 RODBC_1.2-5 [16] Biobase_2.3.11 rcom_2.1-3 rscproxy_1.3-1 loaded via a namespace (and not attached): [1] annotate_1.21.5 cluster_1.11.13 genefilter_1.23.4 GSEABase_1.5.5 [5] RBGL_1.19.2 splines_2.9.0 survival_2.35-4 tools_2.9.0 [9] XML_1.99-0 xtable_1.5-5 Thanks, Fraser

Hi Fraser -- I notice your packages are not in sync with your version of R. Time to update http://bioconductor.org/install so we avoid chasing spurious incompatibilities. Also if the example can be winnowed a bit so that there are fewer packages on the search path that might help to trace the problem. From parsing the code it's hard to see what the problem might be; can you provide the output of showMethods(summary) showMethods(nrow) getClass(class(hyperGTestresult)) after the error occurs? Or perhaps to get your hands dirty, try trace(summary, browser, signature=c(object=class(hyperGTestresult))) and then run the command again. You'll be in the 'browser' at the top of the summary function, ready to step through and examine the values generated at each step. See ?browser for more Martin "Sim, Fraser" <fraser_sim at="" urmc.rochester.edu=""> writes: > Hi, > > I have a new problem with R code that worked under R2.8.1. > > When I run in my code (too long to reproduce): > summary(hyperGTestresult) > > I get the error: > Error in if (nrow(df) == 0) { : argument is of length zero > > Here's the result of: >>hyperGTestresult > Gene to GO BP test for over-representation > 1824 GO BP ids tested (149 have p < 0.001) Selected gene set size: 252 > Gene universe size: 12474 > Annotation package: hgu133plus2 > > So it looks like the hyperGTest worked and found some significant terms. > > I can even extract the GO terms using sigCategories() and the pvalues > using pvalues() but the summary() and htmlReport() methods return the > same error. > > I did not have this problem using the same code in R2.8.1. > >>sessionInfo() > R version 2.9.0 (2009-04-17) > 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] stats graphics grDevices datasets utils methods base > > > other attached packages: > [1] GOstats_2.9.4 graph_1.21.7 Category_2.9.14 > [4] annaffy_1.15.0 KEGG.db_2.2.11 GO.db_2.2.11 > [7] hgu133plus2.db_2.2.11 RSQLite_0.7-1 DBI_0.2-4 > [10] AnnotationDbi_1.5.23 RColorBrewer_1.0-2 gplots_2.6.0 > [13] gdata_2.4.2 gtools_2.5.0-1 RODBC_1.2-5 > [16] Biobase_2.3.11 rcom_2.1-3 rscproxy_1.3-1 > > loaded via a namespace (and not attached): > [1] annotate_1.21.5 cluster_1.11.13 genefilter_1.23.4 > GSEABase_1.5.5 > [5] RBGL_1.19.2 splines_2.9.0 survival_2.35-4 tools_2.9.0 > > [9] XML_1.99-0 xtable_1.5-5 > > Thanks, > Fraser > > _______________________________________________ > 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 -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793