Characteristics of ChIP-chip data. (a) A quantile-quantile plot (QQ plot) for one representative Rap1p ChIP-chip experiment (red) against Gaussian distribution with a standard deviation of 0.35 and a mean of 0 (black bars). The upper and lower bounds of the black dashed line represent extreme values for 10,000 simulated Gaussian distributions with the above parameters. For Rap1 about 92% of the data fit the Gaussian distribution. The top 8% is skewed away from the simulated data. (b) A sliding window analysis for yeast chromosome VI produced by ChIPOTle for four Rap1p replicates . Window size is 1 kilobase (kb) with 0.25 kb step size. The Rap1p binding sites are identified with arrows.