Optimized probe selection method

1. A method for selecting optimized oligonucleotide probes for use in a hybridization-based assay from an original oligonucleotide probe set, the method comprising the steps of:

a) providing the original oligonucleotide probe set on a first and second hybridization array;

b) providing serial dilutions of a genomic sample, wherein the genomic sample is labeled;

c) hybridizing a first dilution of the labeled and serially diluted genomic sample to the first hybridization array, d) measuring a signal intensity produced for each of the probes;

e) hybridizing a second dilution of the labeled and serially diluted genomic sample to the second hybridization array;

f) measuring a second signal intensity produced for each of the probes;

g) computationally generating weighted regression data from the signal intensity produced for each of the probes;

h) entering the regression data into a database; and

i) querying the database to select optimized probes which exhibit signal intensities that correspond to the serial dilutions of genomic sample, are reproducible, and are strong relative to other probes in the original probe set.

2. The method of claim 1 , wherein the oligonucleotide probes are DNA or RNA.

3. The method of claim 1 , wherein the hybridization-based assays are selected from the group consisting of microarray-based assays, bead-based assays, genotyping assays, and RNAi assays.

4. The method of claim 1 , wherein the hybridization-based assays is a microarray-based assay.

5. The method of claim 4 , wherein the microarray is synthesized by maskless array synthesis.