Weighted scoring scheme. The microarray probes consistently identified as methylated candidates on dye-swap arrays were scored 1; similarly unmethylated microarray probes were scored -1. The rest of the microarray probes were assigned a weighted score based on their location on the plot. LRmeth: log likelihood ratio cut-off for methylated loci; LRunmeth: log likelihood ratio cut-off for unmethylated loci. LR: log likelihood ratio on dye-swapped arrays.