Figure 3
Example of the effects over-normalization using global-median normalization. Calling results on an ALL tumor sample (sample 4) after (A) global-median and (B) CGHnormaliter normalization are shown. In these figures normalized log2 intensity ratios and segments are represented by dots and blue horizontal lines, respectively. Aberration probabilities are indicated by the length of the green downward (gain) and red upward (loss) bars. Note that segments are designated gain or loss if their probabilities exceed 0.5. G-banding and FISH analyses revealed gains in 14 chromosomes (4, 5, 6, 7, 8, 10, 11, 12, 14, 17, 18, 21, 22, 23(X)) most of which are confirmed using CGHnormaliter. Over-normalization caused by global-median normalization instead leads to many incorrect calls.