The proposed normalization procedure: (a) The MA plot before normalization shows a need for rotation to correct dye-bias. (b) To determine the correct angle of rotation, the σ(M) vs σ(A) 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.