Fig. 1

a Density of DNAm intensity by probe type. Infinium I and II assays display different β-value distributions (0 indicating unmethylated sites, 1 indicating fully methylated sites), which may lead to results that contain an over-representation of type I probes due to the larger variance of type II assays. This figure shows the distribution of β-values that were obtained from a single peripheral blood specimen collected for women diagnosed with breast cancer. Differences in between probe types (visualized at the ends of the distributions (type I probes—red dotted line; type II probes—blue dotted line)) are adjusted using normalization procedures, which attempt to harmonize the differences in distributions between probe types. b Density of DNAm intensity by the experimental group. The quality of the data for each specimen can be readily visualized using a density plot, which enables one to compare distributions between, for instance, cases and controls in order to identify particular specimens with deviations in their distribution, the latter of which may serve as an indication that the specimen results are of poor quality