R help - Apr 2004 - <no subject>

Dear all,

I want to compute pairwise correlations between all rows of two matrices
where the pairs are formed by taking all rows from each matrix with a common
factor.  In other words, I want to take all pairwise correlations between
rows after stratifying by a factor (the same factor) in each matrix.  More
concretely, I have factor for matrix 1 like:

A
A
B
B
C
E
G

And for matrix 2,

A
B
C
D
E
F
G

And two matrices with the same number of columns.  I want to get
correlations between row 1 of matrix 1 and row 1 of matrix 2, row 2 of
matrix 2 and row 1 of matrix 2, etc.

I just can't seem to get the correct combination of "apply"
functions to do
this.  Any ideas?

Thanks,
Sean