Fig. 6

A global analysis of batch-effect corrections made after various preprocessing. Across each probe in the EpiSCOPE (a) and BFiN study (b), the maximal probe-wise beta difference after batch-effect correction was determined and a density plot constructed. The area under the curve illustrates the maximal level of adjustment across the probe distribution. The two vertical lines highlight probes with 10% and 1% maximal probe-wise beta difference (− 1 and − 2, respectively, in log scale). This is consistent with the segmentation used in Table 1. The rightmost column illustrates that if raw preprocessed data are subset into Type I (grey dashes) and Type II (grey dots) probes, many of the Type I probes had less batch-effect correction adjustment