[BioC] GOHyperG pvalue and expression value,

[Saurin Jani]

Hi BioC,

May be this is basic question,please forgive me for
that...but anyone can help me understand,how GOHyperG
pvalue consider expression intensities in order to
calculate pvalue to make GO Terms more important that
other GO Terms exists on chip or differential
expressed gene set? for instance: Bio Process:

[1] 
GO:0006333 
chromatin assembly or disassembly
2 Genes associated out of my differ. Exp. Genes
pvalue: 0.00110121111270826	
total genes from chip : 16

[2]
GO:0030199
collagen fibril organization
2 Genes associated out of my differ. Exp. Genes
pvlaue: 0.0929493556475916
total genes from chip : 14

GOHyperG function takes unique LLids..and environment
and what GO Term we need information for..! there is
no  argument about expression set? 

Thank you so much in advance,
Saurin