Figure 4.

A screenshot of MethMarker's performance window, summarizing the evaluation of a bisulfite pyrosequencing-based biomarker. In the upper panel, MethMarker displays the optimized regression formula, which predicts - based on measurement values for CpGs number 5 and 18 - whether a sample belongs to the case (that is, is methylated, indicated by positive score values) or to the control group (that is, is unmethylated, indicated by negative score values). Note that the score value is a measure of the probability with which the sample is a case rather than a control, not an estimate of the DNA methylation level (in fact, the probability p can be calculated from the score s with a simple formula: . The center panel displays the results of leave-one-out cross-validation, providing an estimate of the biomarker performance on new data. The diagrams at the bottom visualize the degree of separation between the two classes when plotting the measured level of DNA methylation over the score value of the regression formula (left) and the robustness of predictions in the face of increasing noise levels (right).