[BioC] a simple question

[Weiwei Shi]

Dear Listers:

I have a stat question on the senario like this:
I have 6 genes and 2 biological pathways:
gene 1-3 exclusively belongs to pathway A and gene 4-6 are shared by
pathway A and B. If we observe gene 1-3 are differentially expressed,
we have more confidence to say pathway A is activated in this
situation than the one in which only gene 4-6 are observed to be
differentially expressed. (In both situations, we do not know the
expression levels for the rest genes). Scale up the situation to 1000
genes and 20 pathways for example, what kind of statistical approach
should I use here to differentiate the situations above and is there a
software in R or somewhere doing this?

thanks,

-- 
Weiwei Shi, Ph.D
Research Scientist
GeneGO, Inc.

"Did you always know?"
"No, I did not. But I believed..."
---Matrix III