Patent Document ID: 8521441
Application ID: 11042654
Patent Flag: 1

Claim One:
1. A computer program product embodied on a computer readable storage medium, the computer readable storage medium encoded with computer-executable instructions which, when executed by a processor, cause the processor to execute a method of reducing fluorophore-specific bias in gene expression data comprising: receiving a first plurality, second plurality, third plurality, and fourth plurality of fluorescent emission signals obtained from a two color hybridization microarray experiment comprising steps (1)-(10): (1) 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; (2) 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; (3) 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; (4) 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; (5) 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; (6) detecting said first plurality of fluorescent emission signals at each of a plurality of discrete loci on the first microarray from said first pool of fluorophore-labeled genetic matter that becomes bound to said first microarray under said conditions; (7) detecting said second plurality of fluorescent emission signals at each of said plurality of discrete loci on the first microarray from said second pool of fluorophore-labeled genetic matter that becomes bound to said first microarray under said conditions; (8) 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; (9) detecting said third plurality of fluorescent emission signals at each of said plurality of discrete loci on the second microarray from said third pool of fluorophore-labeled genetic matter that becomes bound to said second microarray under said conditions; and (10) detecting said fourth plurality of fluorescent emission signals at each of said plurality of discrete loci on the second microarray from said fourth pool of fluorophore-labeled genetic matter that becomes bound to said second microarray under said conditions; wherein: said first microarray and said second microarray are similar to each other, exact replicas of each other, or are identical; and said first fluorophore and said second fluorophore are different; wherein the computer readable storage medium comprises computer executable instructions for: normalizing a first fluorescent emission signal by a first mean intensity, said first fluorescent emission signal being measured at a first discrete locus of the plurality of discrete loci on the first microarray, said first mean intensity being the mean intensity of the first plurality of fluorescent emission signals measured at each of the plurality of discrete loci on the first microarray, thereby calculating a first normalized fluorescent emission signal; normalizing a second fluorescent emission signal by a second mean intensity, said second fluorescent emission signal being measured at said first discrete locus, said second mean intensity being the mean intensity of the second plurality of fluorescent emission signals measured at each of the plurality of discrete loci on the first microarray, thereby calculating a second normalized fluorescent emission signal; determining a first color ratio between said first normalized fluorescent emission signal and said second normalized fluorescent emission signal; normalizing a third fluorescent emission signal by a third mean intensity, said third fluorescent emission signal being measured at a second discrete locus of a plurality of discrete loci on the second microarray, said third mean intensity being the mean intensity of the third plurality of fluorescent emission signals measured at each of the plurality of discrete loci on the second microarray, thereby calculating a third normalized fluorescent emission signal; normalizing a fourth fluorescent emission signal by a fourth mean intensity, said fourth fluorescent emission signal being measured at said second discrete locus, said fourth mean intensity being the mean intensity of the fourth plurality of fluorescent emission signals measured at each of the plurality of discrete loci on the second microarray, thereby calculating a fourth normalized fluorescent emission signal; determining a second color ratio between said third normalized fluorescent emission signal and said fourth normalized fluorescent emission signal, wherein the first color ratio and the second color ratio are determined for a same individual component of genetic matter; wherein said first color ratio and said second color ratio have opposite fluorophore bias: computing an average color ratio by averaging said first color ratio and said second color ratio, wherein the first color ratio and the second color ratio are for a pair of hybridization experiments of similar, exact replica, or identical microarrays and the same individual component of genetic matter for both members of the pair, with fluorescent label assignment reversed in one member of the pair, and wherein the averaging reduces fluorophore-specific bias in the average color ratio; wherein said average color ratio is computed by the expression 
 ½(log( r x/y )−log( r x/y (rev) )) by said instructions for computing, wherein r x/y represents said first color ratio and r x/y (rev) represents said second color ratio; and outputting the average color ratio to a user, a user interface device, a monitor, a user-accessible computer readable storage medium, or a user-accessible local or remote computer system; or displaying the average color ratio.