[BioC] Error using summary method on GOHyperGResult object

Sim, Fraser Fraser_Sim at URMC.Rochester.edu
Thu May 14 19:42:50 CEST 2009


I have a new problem with R code that worked under R2.8.1. 

When I run in my code (too long to reproduce):

I get the error:
Error in if (nrow(df) == 0) { : argument is of length zero

Here's the result of:
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.

R version 2.9.0 (2009-04-17)

LC_COLLATE=English_United States.1252;LC_CTYPE=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
 [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     


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