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. 2006 Mar 1;7:100. doi: 10.1186/1471-2105-7-100

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Copyright © 2006 Bengtsson and Hössjer; licensee BioMed Central Ltd.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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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 $A_{1}$ turn into two different densities for the measured data. The (upside-down and dashed) curve at the bottom shows a hypothetical density function, φ_x(·), 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, ${φ_{y_{c}} (\cdot)}_{c}$ , 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.