[BioC] GOStats - HyperGTest - expert opinion needed about the approach selecting gene list

[Srinivas Iyyer]

Dear all,
I am analyzing gene diff. expression data for a rat
chip. 

instead of asking which biological processes (BP) are
enriched for my diff. expressed genes, i am interested
in asking which BP are enriched for upregulated genes
and which BP are enriched for downregulated genes. 

For doing this, i seperated the diff. expressed gene
lists into two lists (up and down regulated) after
filtering the list for p-val 0.001 (this p-val is
obtained from a t-test). 

now I make all up-regulated genes as one 'test list'
to see enrichment for BP using entire 'chip'(genes/BP
on present on chip) as universe. 

Similarly, I check enrichement for all downregulated
genes keeping chip as universe. 

My question is:
1. Is it okay to do this way instead of making all up
and downregulated genes into a one big list. 

2. If i do not see many differential expressed genes,
by doing this way, will I be getting all false
positive enriched terms. 

3. Am I missing any key concept and ending up in a
flawed analysis. 

any suggestions will help me in big way. 

Thank you 








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