Figure 1

Principle for Silhouette scores. Principle for quality assessment of genotyping clusters using Silhouette scores, illustrated for one data point (i). The SNP genotypes have been assigned based on cluster formation in scatter plots with the signal intensity fraction on the x-axis and the logarithm of the signals from both alleles on the y-axis. For each data point (i) in the scatter plot, the Silhouette s(i) is calculated by the formula in the figure, where a(i) is the average distance from i to all data points in the same genotype cluster (green lines), and b(i) is the average distances from i to all data points in the cluster closest to the data point, either b₁(i) (blue lines) or b₂(i) (red lines) [1]. Max and min in the formula denote the largest or smallest of the measures in the brackets. The "average silhouette width" is calculated by calculating the mean of all s(i) for each genotype cluster and the "Silhouette score" for the whole scatter plot (SNP assay) is obtained by taking the mean of the average silhouette width for all clusters.