Hello.
I've been recently working with two color array data and to implement some procedures I'll need to use data from the two channels separately. Thus, I can't really use normalization methods that give a ratio or an average value (such as the ones included in the limma R package), I'll need to normalize the two channels separately and keep them separated. As I mostly use Affymetrix microarrays, I'm stuck, more or less.
Is anyone able to give a hint on how to proceed? Thanks.
