Patent ID: 6916621

Claim:
An array-based method for determining a relative amount of a nucleic acid sequence in two or more samples, the method comprising: (a) contacting a first sample and a second sample with a first array and a second array respectively, the first and second array comprising a plurality of nucleic acid segments, wherein each nucleic acid segment is immobilized to a discrete and known spot on each of a first substrate surface and a second substrate surface to form the first and the second arrays of nucleic acid segments wherein each said spot comprises a nucleic acid sequence that is a marker for each said spot on the array providing a plurality of markers on the array and the nucleic acid segments immobilized on the second array comprise substantially the same plurality of nucleic acid segments immobilized on the first array, each array further comprising at least one calibration spot comprising a mixture of the same plurality of nucleic acid sequence markers present in all of the other spots of the array, the first sample and second sample each comprising a plurality of nucleic acid segments comprising a detectable label wherein contacting is performed under conditions wherein the labeled nucleic acid segments specifically bind to the nucleic acid segment immobilized on the arrays; (b) identifying which spots on the first and the second arrays are specifically bound to a labeled nucleic acid segment and measuring the an amount of label on each spot; (c) comparing the amount of labeled nucleic acid segment specifically bound to immobilized nucleic acid segments on the first array to the amount of labeled nucleic acid segments specifically bound to the same nucleic acid segment immobilized on the second array, and comparing the amount of labeled nucleic acid segments specifically bound to the calibration spot on the first and second arrays: and (d) normalizing the ratio of the amount of label associated with the nucleic acid segments in the first and second arrays by adjusting the ratio by a figure representing the difference between an expected ratio of label associated with the calibration spot on the first and second arrays and a detected ratio of label associated with the calibration spot on the first and second arrays, thereby determining the relative amount of a nucleic acid sequence complementary to a same nucleic acid segment present in the first sample compared to that present in the second sample.