The need for biological replicates. We show smoothed methylation profiles for three normal samples (blue) and matched cancers (red) from the Hansen data . Also shown is the smoothed methylation profile for an IMR90 cell-line (black) from the Lister data . Had we only analyzed normal-cancer pair 3 (thick lines), there would appear to be a methylation difference between cancer and normal in this genomic region. When all three cancer-normal pairs are considered, however, this region does not appear to be a cancer-specific differentially methylated region.
Hansen et al. Genome Biology 2012 13:R83 doi:10.1186/gb-2012-13-10-r83