Equalizing the signal densities of the two channels removes the intensity dependency of the log-ratios for non-differentially expressed genes. Equalizing the signal densities of the two channels remove the intensity dependency of the log-ratios of non-differentially expressed genes. Left: Equal gene-expression distributions in both channels will under the non-channel balanced affine transform turn into two different densities for the measured data. The (upside-down and dashed) curve at the bottom shows a hypothetical density function, φ
(·), of the true (log) gene-expression levels expected to be equal in both samples. The distributions of the affine transformed signals are shown in the (rotated and dashed) density functions, , at the left (red and green curves). The average signal density (middle gray curve) to be normalized toward corresponds to a common measurement function (gray function in the main plot). Right: Normalizing the non-equal densities of the two channels makes the log-ratios of the non-differentially expressed genes zero for all intensities.