Figure 1
From: Comparison of genotype clustering tools with rare variants
Impact of parameters on GenoSNP’s clustering. Impact of the choice of initial parameters on GenoSNP’s clustering of two samples (MHIC04326 shown in (A), (B) and (C), and MHIC06654 shown in (D), (E) and (F)). The first row shows the clustering results of the two samples using the default parameters (25 EM iterations and an initial variance of 0.1). The second row shows the results when keeping an initial variance of 0.1, but increasing the number of EM iterations to 300. The last row shows the results when increasing both the initial variance and the number of EM iterations to 100 and 300, respectively. In all cases, only markers in the BeadPool 1 are kept. Each point represents the raw B allele intensities against the raw A allele intensities (base two logarithm in both cases) of each marker. The AA, AB and BB genotypes are shown in blue, red and green, respectively. Markers that were below the quality threshold of 0.8 are shown in black.