Effect of adjusting for CNV for the LNCaP cell line. Smoothed color density representation of methylation estimates for copy number state 2 derived by BayMeth compared to 450k array beta values. A threshold of 13 was applied for the depth of SssI, which gives 61,969 bins, of which we have for 18,010 100-bp bins a beta value and BayMeth estimate. In addition the y = x line (green dashed line) is shown. Black points indicate outliers. Top left: CNV-unaware BayMeth; top right: CNV-aware BayMeth; bottom left: SssI-free and CNV-unaware BayMeth; bottom right: SssI-free BayMeth. CNV, copy number variation.