Figure 4.

Genotype 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.