Gitschier: You obviously aren't color blind. FISH uses just a single fluorescent probe, so why did you feel the need for a two-color, comparative system for the microarrays?
http://plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000560#article1.body1.sec1.p10

Where did you get your information that FISH uses a single fluorescent probe? One of the beauties of FISH is the ability to multiplex probes with different fluorophores, thereby examining multiple loci simultaneously. For an example see http://www.urovysion.com/Results_359.aspx