[BioC] Fisher exact test

[S Peri]

Dear group, 
 I have log-fold changes from a set of experiments. I
want see the relation between these two experiments in
relation to a pathway. Can I use a fisher exact test
on these two data sets to see different outcomes for
two datsets on one pathway. Is this test valid only
for data in a 2X2 matrix, is this valid for a 2X12K
matrix (2 studies, 12K genes). I apologize if this is
a wrong question to ask here. 
Peri.