Simple scatter plots for SNP rs12466929 (A/G) from 50-plex data set (this SNP is representative of the entire set of 50 HapMap SNPs). For each plot the x-axis represents signal values for X allele (A for this SNP) and the y-axis represents signal values for Y allele (G for this SNP). All values are in log scale. Magenta, green, blue and black coloured symbols denote the classes YY (GG), YX (AG), XX (AA) and NN (negative control samples), respectively. Plot (1) combines the two ASO-APEX Left probes (one for each allele); plot (2) combines the two ASO-APEX Right probes (one for each allele); plot (3) is for the APEX Left probe; plot (4) is for the APEX Right probe. All the classifiers except APEX Left (plot 3) give well separated genotype clusters for this SNP. Dynamic variable selection is able to automatically weight these LDA classifiers in such a way that the homozygous AA cluster in plot (3) (blue) is able to contribute to the final call for such genotypes, even though AG (green) and GG (magenta) genotype clusters overlap somewhat for this Left APEX probe. Additional file 11 shows four-panel scatter plots for all 50 SNPs from the 50-plex data set.