global normalization

Hello all,
I have question about global normalization.
I have data from big experement(two-color cDNA arrays) where used three
different layouts but the same set of genes. 
I used limma package for within array normalization.
My question is: how I can do between array normalization (global) if arrays have
different layout(different location and different number technical replicates
(number of spots of a gene on an array))?  

Sincerely, Natalia.