Analysis of methylation using nucleic acid arrays

A method of selecting probes to be included in an array of probes comprising:

• identifying a plurality of CpG islands wherein said plurality comprises more than 10,000 different CpG islands in the genome of a single organism;
• defining the ends of each CpG island and thereby identifying a probe selection region for each CpG island in the plurality;
• selecting a probe set for each probe selection region, wherein the probes in each selected probe set are perfectly complementary to the probe selection region targeted by that probe set;
• assessing a probe set score for each selected probe set, wherein the probe set score equals 0.18× the number of probes in the set;
• and
• for each selected probe set having a probe set score of less than 1.44, extending the probe selection region by 150 bps at either end and then selecting a probe set from the extended probe selection region,
• wherein each of the steps of identifying, defining, and selecting is performed by a computer, and wherein the computer that performs the identifying step is programmed to define a CpG island as a genomic region that is at least 200 bases in length and has a GC content of at least 50%.