Figure 2

Improvements in replication for the EBV data set. (a) ROC curves for replication between a discovery and a validation data set. The validation data set was constructed to show in silico batch effects. The dotted and solid lines represent, respectively, the commonly used false discovery rate cutoffs of 0.01 and 0.05. (b) Concordance curves showing the percentage overlap between the top k DMPs in the discovery and validation cohorts. Additional normalization methods are assessed in Additional file 1: Figure S3. Functional normalization shows a high degree of concordance between data sets. (c) The percentage of the top 100,000 DMPs that are replicated between the discovery and validation cohorts and also inside a differentially methylated block or region from Hansen et al. [38]. DMP, differentially methylation position; EBV, Epstein–Barr virus; Funnorm, functional normalization; ROC, receiver operating characteristic.