Our initial goal was to analyze the data in an unbiased manner, in order to identify variations in DNA methylation that were demonstrated by the data, rather than our preconceptions about the samples and/or DNA methylation. Preliminary clustering of all samples and all probes resulted in separation of male and female samples based on the methylation state of the X chromosome, consistent with our previous findings (Bibikova et al., 2006). We therefore examined X chromosome and autosomal probes separately.
