Figure 3

Impact of preprocessing on signal and noise. Plot showing the cluster centers (A) and variability (B) after various pre-processing methods have been applied. Values were obtained using the independent genotype calls available from the HapMap database for the majority of SNPs. Quantile with loess, which we saw in Figure 2C removes intensity-dependent curvature from the log-ratios, does so at the cost of increasing the variability for some homozygous calls. Results plotted are from the Omni1-Quad platform.