normalize different tissue types

[Skov]

Hi,

I have a microarray experiment with two different tissue types, 16
chips from human adipose tissue and 16 chips from human skeletal
muscle. From the litterature, we know that there are signals going
from adipose tissue to skeletal muscle and therefore I want to see if
there is a correlation between significantly regulated genes between
these two tissues.

However, I dont know if I should normalize all arrays together or I
should normalize the two tissue types separately.

Hope that you can help me and thanks in advance.

Best,
Skov