Hi,

I need a precision about columm "size" in out of hyperGtest ( Gostat package)

In https://stat.ethz.ch/pipermail/bioconductor/2006-December/015346.html
we can read: "The "Size" column is the number of genes annotated at the given GO
term (where genes are restricted to the defined gene universe)"
Hence, for a given Term and given platform, we must have a constant number.

I explain: 
first set data :  A contains 687 probesets
I practise a hyperGotest:
This is an extract from the result:
GOBPID       Pvalue OddsRatio    ExpCount Count Size     Term

36  GO:0008283 0.0180640706  1.913970  8.20236088    15  266     cell proliferation

If I inderstand well: 266 probesets on affy HGU133.2.plus are annotated "cell proliferation"


Then, 

I practise the same analysis on a second set (B) , inclusive of A :  414 probesets

result :
    GOBPID    Pvalue OddsRatio    ExpCount Count          Size        Term

20 GO:0008283     0.008295992  1.765957         14.97834828    25                         745                 cell proliferation

Here, that's mean that 745 probesets are annotated "cell proliferation"



Why the number of size for the same term is not the same?

Moreover, B being inclusive of A , the 25 probesets annotated "cell proliferation " , discovered in B analysis are reduced to 15 probesets in A analysis. Normally, in A analysis, I should have at least 25 probesets annotated "cell proleferation".

Why didn't I find at least 25 probesets in A analysis ?




Thanks 
Greg


> sessionInfo()
R version 2.8.1 (2008-12-22) 
i386-pc-mingw32 

locale:
LC_COLLATE=French_Canada.1252;LC_CTYPE=French_Canada.1252;LC_MONETARY=French_Canada.1252;LC_NUMERIC=C;LC_TIME=French_Canada.1252

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

other attached packages:
 [1] GOstats_2.8.0        Category_2.8.4       genefilter_1.22.0    survival_2.34-1      RBGL_1.18.0          annotate_1.20.1      xtable_1.5-4        
 [8] graph_1.20.0         GO.db_2.2.5          hgu133plus2.db_2.2.5 RSQLite_0.7-1        DBI_0.2-4            AnnotationDbi_1.4.3  Biobase_2.2.2       

loaded via a namespace (and not attached):
[1] cluster_1.11.11 GSEABase_1.4.0  XML_1.99-0 


      
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