Simulated ChIP-Seq experiment. A: MA-plots for simulated peaks; Each dot corresponds to a single peak. Black dots, green circles and purple crosses indicate unchanged sites, sites with changed profiles and sites with affinity changes, respectively. The left plot shows changes in base affinity in treatment vs control as a function of mean peak affinity, no biological variability and no sequencing effects are considered. In contrast, the right panel results if biological variance (Gamma distributed) and sampling of reads (Poisson distributed) are simulated. In this case, sites with unchanged base affinity may still show substantial fold changes, which hampers the detection of true differential sites. The filled green circle marked by an arrow corresponds to the profile depicted in detail in B: Simulated example profiles (mixtures of two Gaussian curves) with profile change simulated as a change in the mixing parameter. Left panels correspond to the control condition, right panels to the treatment condition. First row shows three peak profiles for each condition and the area under the curves integrates to 1. Within each condition there is a small degree of variability regarding the position and width of the two sub-peaks and also their relative strength. Between conditions the mixing parameter changes substantially. In the middle row, each of the six profiles is weighted with the sample specific affinity value for the given peak. The areas under the curves now vary between samples. In the bottom row, the sequencing process is simulated with a Poisson distribution resulting in histograms of reads mapping along the extend of the peak. C: Receiver operator characteristic (ROC) curves for various methods. Left: only unchanged sites and sites with profile changes are considered; Right: only unchanged sites and sites with affinity changes are used. Circles indicate the considered operating point (FDR=0.05).