Fig. 5

This diagram illustrates the method used by MethylCallR to account for duplicated probes in EPICv2. The process involves selecting unique probes (green box) based on the criteria of MethylCallR (red dotted box) from all duplicated probes (gray box). The remaining probes are used to generate the Address_chain_file. A list of the removed probes can be found in Duplicated.Probes.preset (orange box). A summary of the duplicated probes is provided in the gray box ((i) exactly duplicated probes (11,354 probes), (ii) duplicated probes in the probe sequence (1,000 probes), and (iii) duplicated probes in position (268 probes)).