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.
Lin et al. Genome Biology 2008 9:R63 doi:10.1186/gb-2008-9-4-r63