Patent Document ID: 9223929
Application ID: 11376398
Patent Flag: 1

Claim One:
1. A method of processing affinity-based array data, comprising: (a) determining an estimate of a probe and a target interaction in an array comprising (i) analytical expression and (ii) by calibration of the array using at least one standard probe; (b) generating a stochastic-matrix that utilizes the estimate in a Markov chain model that comprises modeling hybridization, cross-hybridization, and unbound transition probabilities between states; (c) obtaining optical affinity-based array data using a light detection device; (d) applying the array data to the stochastic-matrix; (e) applying an optimization algorithm selected from the group consisting of a maximum likelihood estimation algorithm, a maximum a-posteriori criterion, a constrained least squares calculation, and any combination thereof that exploits and does not suppress non-specific interactions by considering the non-specific interactions as interference rather than noise; and (f) outputting optimized affinity-based array data to a user, wherein the optimized affinity-based array data has an improved signal-to-noise ratio compared to the array data obtained by using the light detection device; wherein at least one of the steps (d)-(f) is executed by using a suitably programmed computer.