Figure 3

Genome-wide reproducibility within and between ChIP-chip and ChIP-seq replicate profiles. (a) Genome-wide reproducibility between two profiles was measured by Pearson's correlation coefficient, r, between their signal intensities (in 1 kb bins). Both ChIP-chip and ChIP-seq have high reproducibility (median r≈0.83), whereas the reproducibility between replicate ChIP-chip and ChIP-seq profiles is moderate (median r≈0.41). This figure also shows one typical example of genome-wide correlation between biological replicates of (b) ChIP-chip and ChIP-chip, (c) ChIP-seq and ChIP-seq, and (d) ChIP-chip and ChIP-seq. A locally weighted scatterplot smoothing (LOESS) regression line is also shown in each of these plots.