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Distribution of signal intensities before and after normalization. Panels depict the distribution of Cy5 (red) and Cy3 (green) signal values before normalization (a), after within-array normalization (b), and after between-array normalization (c) in LIMMA. Since replication timing is a relative property, equivalent amounts of DNA are transcribed before and after the middle of S-phase, allowing distributions to be transformed to a common scale for each channel (b) and array (c).
