Smoothed scatter plots of log-ratios versus average intensities for a sample run in replicate. This figure gives an example of signal from a good quality array (A), with three well-separated clusters of points which approximately correspond to the AA (top cluster), AB (middle cluster) and BB (bottom cluster) genotypes. Signal from the same sample which is clearly of very low quality is also shown (B). In this plot we see one cluster of points, rather than the expected three. This major cluster occurs at low intensity (≈6), which is also highly unusual (intensities between 8 and 14 on the log2-scale are typical). In each panel, non-normalized log-ratios (M) are plotted on the y-axis versus average intensities (S) on the x-axis.