Figure 4 | Scientific Reports

Figure 4

From: Sandcastle: software for revealing latent information in multiple experimental ChIP-chip datasets via a novel normalisation procedure

Figure 4

Examples of how the normalisation procedure affects real ChIP-chip datasets.

Data following each stage of the procedure are shown on each line (raw data, quantile normalisation applied, pseudo-modal shift applied, scaling applied). The first column shows all untreated (black line) and UV treated (red line) H3Ac binding datasets. Following the quantile normalisation step the replicate datasets follow the same overlapping distributions, hence only two visible lines. The second column shows a selected single untreated H3Ac dataset (black line) along with data mirrored about the zero point (red dashed line) and the SND over this same range (blue dotted line). The third column shows the same data as Q-Q plots, along with the position of the SND (blue dotted line), with data points below zero highlighted (grey box). These graphs show the estimated background region of the fully normalised data closely match the SND. All density plot x- and y-axes show ratio and density values respectively. All Q-Q plot x- and y-axes show theoretical and sample quantiles respectively.

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