Figure 1

Normalised and summarised allele intensities from the Illumina BeadChip array. The intensities are shown in transformed polar coordinates: the theta-coordinate represents the angle from the x-axis (the angle from the x-axis to the vector [A, B] of the two allele intensities), and the R-coordinate represents the copy number (the length of the vector). (A) Intensities for a single nucleotide polymorphism (SNP) from 120 arrays, clearly separating the intensities into three groups (A/A, A/B, B/B). (B) Data from 317,000 SNPs (from the same 120 arrays). This plot clearly indicates that signal strength varies considerably with the SNP, a factor that must be taken into account when genotyping individual SNPs and deriving copy numbers. The figure is reproduced with the permission of Gunderson et al. [15]