[BioC] How to get affyId from GOstats output

alex lam (RI) alex.lam at bbsrc.ac.uk
Tue Mar 18 17:59:46 CET 2008

Dear colleagues,

After running hyperGTest, summary(hgOver) returns a table of GO IDs,
Pvalues, Count ...etc

For example, for a particular GO term the Count = 3 and Size = 9. How do
I retrieve the affyIDs of those 3 and 9 genes?

Many thanks,

> sessionInfo()
R version 2.6.1 (2007-11-26) 

LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252

attached base packages:
[1] splines   tools     stats     graphics  grDevices utils     datasets

[8] methods   base     

other attached packages:
 [1] GOstats_2.4.0       Category_2.4.0      genefilter_1.16.0  
 [4] survival_2.34       RBGL_1.14.0         graph_1.16.1       
 [7] annotate_1.16.1     xtable_1.5-2        GO.db_2.0.2        
[10] rae230a.db_2.0.2    AnnotationDbi_1.0.6 RSQLite_0.6-7      
[13] DBI_0.2-4           Biobase_1.16.2     

loaded via a namespace (and not attached):
[1] cluster_1.11.9  rcompgen_0.1-17

Alex C. Lam
Roslin Institute (Edinburgh)
EH25 9PS
United Kingdom
Tel: +44 131 5274471

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