To determine if the mean level of methylation at each CpG dinucleotide site differed between case and control subjects, two different tests were performed. First, the mean of the forward and reverse values was calculated for each CpG site for each sample. A t-test was performed using these mean values to examine differences between case and control groups at each CpG site. Since there were two measurements for each individual, logistic regression using generalized estimating equations (GEE), which accounts for the correlation between the forward and reverse measurements, was also performed (Halekoh and Hojsgaard, 2006). Both these tests were two tailed tests.
