Patent ID: 7226734

Claim:
A method of decoding an array so as to determine the location of a capture probe that has been randomly distributed on the array, said method comprising the steps of: a) providing an array comprising a plurality of distinct capture probes, wherein said capture probes are randomly distributed on said array; b) performing a hybridization step in which said capture probes are hybridized with a plurality of sets of decoder probes, wherein each of said sets of decoder probes comprises a different label, each different label producing a different signal; c) detecting the signal produced by the hybridization step at a location on said array; d) performing a dehybridization step; e) performing an additional hybridization step in which said capture probes are hybridized with a plurality of sets of decoder probes, wherein each of said sets of decoder probes is different from said sets of decoder probes used in the previous hybridization step, and wherein each of said sets of decoder probes comprises a different label, each different label producing a different signal; f) detecting the signal produced by the additional hybridization step at said location; g) repeating steps d-f for a number of stages sufficient to generate a code comprising the sequence of signals detected at said location, said code indicative of the capture probe present at said location; and h) decoding said array with said code.