λlocal is also effective in capturing the local genomic bias from a ChIP sample alone when a control is not available. To demonstrate this, we applied MACS to FoxA1 ChIP-Seq and control data separately. Using the same parameters, all the control peaks are, in theory, false positives, so the FDR can be empirically estimated as Number of control peaks / Number of ChIP peaks. To identify 7,000 peaks, the FDR for MACS is only 0.4% when a control is available and λlocal is used. To get 7,000 peaks when a control is not available, the FDR could still remain low at 3.8% if MACS estimates λlocal from the ChIP sample, whereas it would reach 41.2% if MACS uses a global λBG. This implies that the λlocal is critical for ChIP-Seq studies when matching control samples are not available [5,9].
