Evaluation of the differentialy methylated regions finder. (a) Specificity plotted against sensitivity for the BSmooth DMR finder (black) and a method based on Fisher's exact test (orange) applied to the Hansen data. The gold-standard definition is based on mean differences. Details are explained in the text. (b) As (a), but using a gold-standard definition accounting for biological variation. (c) Comparison based on the association between gene expression and methylation changes in the Tung data. For DMR lists of varying sizes (x-axis), the log2-odds ratios of finding a DMR within 5 kb of the transcription start site of a differentially expressed gene (FDR ≤5%) compared to genes not differentially expression (FDR ≥25%) are shown. FP, false positive; TP, true positive.
Hansen et al. Genome Biology 2012 13:R83 doi:10.1186/gb-2012-13-10-r83