Figure 5.

Effects of tQN on copy number estimates across different Infinium platforms. (a) Effect of tQN on log R ratio response to CNAs compared to BeadStudio data for 36 tumor samples. For each sample the mean difference in segmented log R ratio between BeadStudio and tQN data is plotted. For segments with log R ratio > 0 (red) the difference is BeadStudio minus tQN. For segments with log R ratio < 0 (green) the difference is tQN minus BeadStudio. A positive difference therefore corresponds to a better log R ratio response to CNAs for BeadStudio normalization compared to tQN for both types of segments. Error bars for each sample show the IQR of the difference. Horizontal bars denote the investigated data sets, urothelial tumors from data set 4 (black), breast/colon tumor samples from data set 8 (white), CLL samples from data set 7 (blue) and breast tumors from data set 6 (red). Only segments > 20 SNPs have been included. Segment definition was based on breakpoints from segmentation of BeadStudio copy number data. The small difference in segmented values between BeadStudio and tQN data indicates that tQN does not affect the log R ratio response to CNAs. (b) Boxplots of sample adaptive thresholds for BeadStudio normalized data (white) and tQN data (red) for 6 data sets. Top axis indicates the number of samples in each data set. tQN results in lower sample adaptive thresholds in four out of six data sets and equal thresholds in the remaining two. (c) tQN copy number estimates for chromosome 1 for urothelial tumor UC152_I with individual SNPs colored according to genotype calls: AA (green), AB (yellow), BB (red) and no calls (gray). CNV probes have been removed. tQN removes the asymmetry between AA and BB SNPs for regions of gain and loss observed in BeadStudio normalized data (compare to figure 1d).