Figure 3

Histograms of intensities. (a) Histogram of single-channel log-intensity values for a single array from 28256_Input [12]. The red bars represent the log-intensities for the probes with G+C less than 20, indicating that the bimodal behavior is caused by the GC content of probes. (b) Density plot of single channel log-intensities for two channels on the same array (28256_ChIP, black; 28256_Input, red). Notice that both the scale and the mean of the individual channels must be adjusted to properly normalize the arrays. (c) The raw data log-ratio values (28256_ChIP/28256_Input) for the same array in (b). Note that the 'bump' at 0 is not caused by enrichment but by lack of channel specific normalization of the data.