Peak detection and false discovery rate.

<p>As expected the number of peaks and their width are reduced as coverage is reduced. A) The mean number of peaks identified for each sample by multiplex level. B) The mean peak width of identified peaks for each sample by multiplex level. C) The false discovery rate (FDR) for each sample was computed by contrasting the input to the IP samples: ~181 million (M) reads (blue), ~43M reads (green), ~43M reads chip-2x input (red), ~31M reads (orange), ~21M reads (salmon). FDR for some experiments related to Input-4 are close to >0.45% suggesting these rates are an artifact of the library. Overall, experiments either 1-plex or multiplexed, with equal fractions of IP and input or double input, the FDR is < = 0.43%.