Figure 4From: Validation and extension of an empirical Bayes method for SNP calling on Affymetrix microarraysGenotype regions. These plots display the space on which clusters are assigned genotypes. Colors represent HapMap gold standard calls; numbers represent the calls made by the array algorithms. For SNP SNP_A-1676170, (a) BRLMM genotype regions are shown in the Contrast Center Stretch (CCS) space. The x-axis is a contrast measure that captures the relative intensity difference of allele A with B. The y-axis is related to the average intensity from the A and B alleles. See the BRLMM white paper for more details [22]. For the same SNP, (b) CRLMM regions are plotted. The log ratios of allele A to allele B from intensities derived from probesets of the sense (y-axis) and antisense (x-axis) orientation are shown (that is, M+ versus M- plot). The ellipses represent the cluster regions obtained from the HapMap training set.Back to article page