Figure 3.

Effects of quantile normalization on allelic intensity ratios. Two urothelial carcinomas, UC456_R and UC152_I, analyzed using Infinium 370 k BeadChips are shown. SNPs have been colored based on individual genotype calls: AA (green), AB (yellow), BB (red), CNV probes (blue) and no calls (gray). Horizontal dashed lines represent BAF 0.05, 0.1, 0.5, 0.9 and 0.95, respectively. (a) BeadStudio normalized B allele frequency profile for chromosome 9 of UC456_R. (b) QN normalized B allele frequency profile for chromosome 9 of UC456_R. Compared to BeadStudio (a), QN increases variation for SNPs close to 1 in BAF and decreases variation for SNPs close to 0 in BAF. (c) tQN normalized B allele frequency profile for chromosome 9 of UC456_R. Application of a threshold for the increase in intensity of X and Y by QN lowers the variation of SNPs close to 1 in BAF compared to QN alone (b), and creates BAF values that are more symmetrical around BAF = 0.5 compared to BeadStudio (a). (d) tQN normalized B allele frequency profile for chromosome 1 of UC152_I. The region 1q32.1 to qter discussed in the text is highlighted with a light blue background. CNV probes have been removed.