Figure 2

Bias in the log-ratios introduced by the affine transform. Left: Bias in the log-ratios introduced by the affine transform ${\mathcal{A}}_1$. Each line displays the relationship between the observed and the true log-ratios at a certain (observed) log-intensity A. Each curve is marked with the value of A. We have chosen to truncate the curves when the signals become saturated and the labels for those curves are positioned approximately where they have been truncated. For low intensities there is a great bias (deviance from the diagonal line), especially for large fold changes. At higher intensities the bias is smaller. The curves intersect at the one fold-change level that is independent of the intensity. Right: Real-world example of log-ratios for non-normalized versus affine normalized (with 5% negative) signals. The affine parameters are (${\widehat{a}}_G$, ${\widehat{a}}_R$, log₂$\widehat{\beta }$) = (45.7, 27.0, -0.418). To clarify the intensity-dependent effect only data points close to A = 0.0, 0.5,...,16 are shown.