Figure 1
From: Direct ChIP-Seq significance analysis improves target prediction
dIP significance estimates for bound genomic regions depend on both experiments (IP) and control. Significance is evaluated using the number of IP fragments (magnitude) after conditioning for the total number of fragments aligned to the region (amplitude) in both IP and control. (A) Minimum magnitudes for NANOG and SOX2 IP as a function of the amplitude to obtain FDR ≤ 0.1. (B) Minimum magnitude (m min ) for a fixed amplitude is the magnitude necessary for achieving statistical significance at a given FDR cutoff. It is calculated as that value of m at which the % of cumulative regions just crosses the FDR value. Here we present IP read count for regions with amplitude 20 in NANOG ChIP-Seq data.