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Third: Finally, with Brig's help I performed supervised normalization of DNA methylation data. First, he suggested to focus only on methylated probed, because unmethylated probes, similarly to mismatch probes on old Affymetrix array are confusing and don't provide any additional information.
In fact the unmethylated probes show overall higher intensity than methylated probes (this was first pointed out by Josh Millstein in our discussion of normalization approaches).
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