1. A method of fluorophore bias removal comprising the steps of: (a) labeling a first pool of genetic matter, derived from a biological system representing a baseline state, with a first fluorophore to obtain a first pool of fluorophore-labeled genetic matter; (b) labeling a second pool of genetic matter, derived from a biological system representing a perturbed state, with a second fluorophore to obtain a second pool of fluorophore-labeled genetic matter; (c) labeling a third pool of genetic matter, derived from said biological system representing said baseline state, with said second fluorophore to obtain a third pool of fluorophore-labeled genetic matter; (d) labeling a fourth pool of genetic matter, derived from said biological system representing said perturbed state, with said first fluorophore to obtain a fourth pool of fluorophore-labeled genetic matter; (e) contacting said first pool of fluorophore-labeled genetic matter and said second pool of fluorophore-labeled genetic matter with a first microarray under conditions such that hybridization can occur, and determining a first color ratio between said first pool of fluorophore-labeled genetic matter that binds under said conditions to said microarray and said second pool of fluorophore-labeled genetic matter that binds under said conditions to said microarray; (f) contacting said third pool of fluorophore-labeled genetic matter and said fourth pool of fluorophore-labeled genetic matter with a second microarray under conditions such that hybridization can occur, and determining a second color ratio between said third pool of fluorophore-labeled genetic matter that binds under said conditions to said microarray and said fourth pool of fluorophore-labeled genetic matter that binds under said conditions to said microarray; and (g) computing an average color ratio by averaging said first color ratio and said second color ratio.