[BioC] two color arrays normalization

[Giusy Della Gatta]

Hi everybody,

I am analyzing two color Agilent microarrays
by using LIMMA package.
In my specific case the red channel is representing
"the reference" while the green channel is "the treatment".
Is it enough to use the Target File composition to specify the name of  the samples
and their corrispondet channels?  Or I have to use other specific commands
to specify the "swapping" of the colors?

Thank you in advance!
Regards
Giusy