The proposed normalization procedure: (a) The MA plot before normalization shows a need for rotation to correct dye-bias

<p><b>Copyright information:</b></p><p>Taken from "Normalization and experimental design for ChIP-chip data"</p><p>http://www.biomedcentral.com/1471-2105/8/219</p><p>BMC Bioinformatics 2007;8():219-219.</p><p>Published online 25 Jun 2007</p><p>PMCID:PMC1913544.</p><p></p> (b) To determine the correct angle of rotation, the () vs () plot of the differences between probes is generated (the differences were taken between probes that are 800 bp along the chromosome; see Figure 8). This circumvents the effect of binding signal in determining the rotating angle for original MA plot in (a). (c) The MA plot after rotation by the angle determined in (b). The green line is the lowess fitting line after rotation. (d) The MA plot after lowess normalization. 3000 sample points from each of X and 2L chromosomes are shown

The Scatter plot of ChIP-chip versus mock control after rotation and lowess normalization (cf

<p><b>Copyright information:</b></p><p>Taken from "Normalization and experimental design for ChIP-chip data"</p><p>http://www.biomedcentral.com/1471-2105/8/219</p><p>BMC Bioinformatics 2007;8():219-219.</p><p>Published online 25 Jun 2007</p><p>PMCID:PMC1913544.</p><p></p> Figure 3), (a) without and (b) with running median smoothing. The optimal line for separating the X-specific signals from the 2L signals is now a horizontal line. This suggests that mock control data correction may be neglected when a proper normalization is carried out