Figure 2
Intensity transformations of X and Y by quantile normalization. HapMap sample NA06985 hybridized on an Infinium 370 k BeadChip is shown. SNPs have been colored based on individual genotype calls: AA (green), AB (yellow), and BB (red). SNPs without genotype call are excluded. (a) Scatter plot of BeadStudio allele intensities X and Y. A lowess regression line for heterozygous SNPs is superimposed (solid) together with the expected X = Y line (dashed) illustrating that the dye intensity bias affects heterozygous SNPs. (b) MR plot of BeadStudio allele intensities for chromosome 8 with superimposed lowess regression lines (solid) for each genotype population and locally fitted linear regression lines (dashed blue). The mean M value for each genotype population is indicated by horizontally dashed black lines. (c) MR plot of quantile normalized allele intensities for chromosome 8 with superimposed lowess regression lines (solid black) and locally fitted linear regression lines (dashed blue) for each genotype population, separately. (d) Scatter plot of the intensity transformation XQN/X vs X from quantile normalization. SNPs are colored by genotype. SNPs with low X intensity values (predominantly genotyped as BB) are increased significantly in intensity by QN. (e) Scatter plot of the intensity transformation YQN/Y vs Y from quantile normalization. SNPs are colored by genotype. (f) Histogram of BeadStudio X intensities. (g) Histogram of BeadStudioY intensities.