Bias of LNCaP methylation estimates compared to 450k array beta values. Box plots for bias (estimated methylation level minus 450K array beta value) for BALM (white), MEDIPS (yellow), Batman (orange), CNV-unaware and SssI-free BayMeth (light blue), CNV-unaware BayMeth (dark blue), SssI-free but CNV-aware BayMeth (light red) and CNV-aware BayMeth (red) stratified by copy numbers 2 to 5. (Outliers are not shown.) The width of the boxes is proportional to the percentage of bins (the legend gives the absolute numbers) for the copy number class. A uniform prior for the methylation level was used taking SssI information into account. In the SssI-free version a Dirac-Beta-Dirac mixture with weights fixed to 0.1, 0.8 and 0.1 was used. The results are shown genome-wide for 100-bp bins with at least 75% mappability and where the true methylation estimate is larger than 0.5. A threshold of 13 was applied for the depth of SssI. The blue dashed line indicates a bias of zero. CN, copy number; CNV, copy number variation.