[BioC] comparing different experiments

[Julia Engelmann]

Hi list,

I wonder if I can compare Affymetrix arrays of the same type (ATH1) 
which were made in different laboratories and with different tissue 
types and different references. I have: "tissue1 treated", "tissue1 
untreated" from one lab and "tissue2 treated", "tissue2 untreated" from 
the other lab.
The references (untreated) are  different because of the different 
tissue types. I am interested in the difference between tissue1 treated 
and tissue2 treated, so I thought I could use limma to make a contrast: 
(tissue1_treated-tissue1_untreated)-(tissue2_treated-tissue2_untreated). 
I am not sure if this is valid, though? For example, I do not account 
for the different labs that way.
Maybe it is just possible to analyse each experiment by itself and 
compare the results at a latter stage, say compare lists of 
differentially expressed genes?

Any advice, comments or hints are highly appreciated,

Julia