[BioC] How to get affyId from GOstats output

[James W. MacDonald]

Hi Alex,

See ?probeSetSummary. You might be interested in hyperGoutput() in the 
affycoretools package.

Best,

Jim



alex lam (RI) wrote:
> 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,
> Alex
> 
>> sessionInfo()
> R version 2.6.1 (2007-11-26) 
> i386-pc-mingw32 
> 
> locale:
> LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
> Kingdom.1252;LC_MONETARY=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)
> Midlothian
> EH25 9PS
> United Kingdom
> Tel: +44 131 5274471
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623