Figure 2.

Comparison of Batman-analyzed MeDIP-chip data with bisulfite-PCR sequencing data from the Human Epigenome Project (a) Plot of MeDIP-chip data against CpG coupling factor, with points colored by methylation values from the HEP bisulfite-sequencing data. All probes that did not overlap at least one CpG annotated in HEP were excluded. (b) Comparisons of MeDIP-chip data with HEP using a range of processing strategies: LOESS-normalized log₂-ratios in a 100bp window centered around a 50mer probe that overlaps a HEP amplicon (top left), simple averaging of the LOESS-normalized log₂-ratios for all probes within a 500bp window (top right), averaging of the LOESS-normalized log₂-ratios for all probes within a 500bp window and then dividing by the observed/expected CpG density (bottom left), Batman analyzed (bottom right). This analysis was derived from 1481 MeDIP-chip probes that overlapped 667 bisulfite-PCR amplicons from the HEP. HEP methylation values for all CpGs that overlapped any given 100bp MeDIP-chip window were averaged. Furthermore, to reduce noise in the HEP dataset, all 100 bp windows were required to have at least 2 HEP scores (i.e. data from the top and bottom bisulfite-PCR strands for windows containing a single CpG site, or from at least 2 different CpG sites) that differed by <50%. The purple – yellow (0 – 30) color bar on the right of each figure shows the total CpG coupling factor for each probe (c) Comparison of Batman-quantified MeDIP data with bisulfite data from HEP. Points show the mean Batman output for regions with a given HEP methylation level. Error bars show 95% bootstrap credible intervals.