Figure 2.

Comparison of inter-replicate data including our own previously published manual ChIP-seq datasets for CEBPA. (A) Proportional Venn diagram displaying overlap from the union of peak-sets from published manual data and AHT-ChIP-seq for CEBPA. (B) Principal component analysis with automated ChIP-seq data sets (greens) and manual data set (blue). (C) Scatter plot of percent enrichment (y-axis) versus number of peaks identified by MACS (x-axis). The Pearson correlation is shown in the upper left corner. AHT-ChIP-seq data sets are indicated in green shades, and manual data sets in blue. (D) Scatter plot of aligned reads from the automated ChIP-seq data (y-axis) versus number of peaks identified by MACS (x-axis). Pearson correlation in upper left corner. (E) Fraction of unique peaks for each replicate and those that are represented across multiple experiments. Peaks that occur in only one replicate are shown in red, those that occur in at least two replicates in grey, and those which occur in at least three triplicates in black. Mmu1 to Mmu5 refer to biologically individual mice (Mus musculus).

Aldridge et al. Genome Biology 2013 14:R124   doi:10.1186/gb-2013-14-11-r124
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