[BioC] Error using summary method on GOHyperGResult object

[Martin Morgan]

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
>
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-- 
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