Log intensity ratios (allele A versus B), denoted with M, for all SNPs on one chip plotted against average log intensity S values. Both sense and antisense values are shown in all plots. A scatter-plot of these data would include 500,000 points and thus would be hard to interpret. We therefore show two-dimensional histograms with dark and light shades of blue indicating the existence of many and few points, respectively. (a) High quality array. (b) Low quality array.