Red and green channel intensity files were obtained for each sample in the “idat” file format. These files were processed and normalized using the minfi Bioconductor package in R20. Red and green intensities were mapped to the M(eth) and U(nmeth) channels, and the average intensity for these channels were used to check for low quality samples (0 samples were dropped). Intensities from the sex chromosomes were used to predict sex, and we dropped 8 samples that had predicted sex different from its recorded value (indicating potential sample swaps). Then, the M and U channels were subsequently across-sample quantile normalized using an approach developed by Aryee, et al.20. Briefly, this approach forces the distribution of type I and type II to be the same by first quantile normalizing the type II probes across samples and then interpolating a reference distribution to which the type I probes are normalized, stratified by region (e.g. promoter, shore, island, shelf), which has previously been shown to best minimize the variability between replicates20. For all analyses, we retained a single array in the case of duplicates by choosing the sample that had the closest quality profile (via M and U signal intensity) to all other arrays.
