[BioC] Error using summary method on GOHyperGResult object
Sim, Fraser
Fraser_Sim at URMC.Rochester.edu
Thu May 14 19:42:50 CEST 2009
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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