Figure 5

Parallel translation normalization of affine transformed data. Parallel translation normalization of ${\mathcal{A}}_1$ transformed data. The optimal amount of normalization shift in the raw data is a = 220, which corresponds to an effective shift of (${a^{\prime }}_G$, ${a^{\prime }}_R$) = (420, 240). Left: Log-ratios as a function of log-intensities for certain fold changes. The r = 1 curve (dot-dash blue) is horizontal, that is, for this specific value of r and a the log-ratios are independent of the log-intensities. Right: Normalized log-ratios versus true log-ratios. From this graph it is clear that we obtain the minimum error in log-ratios at zero-fold change.