The breast cancer S1514. (a) The points are normalized log2ratios. The BACs are ordered by position in the genome, beginning at 1p and ending at Xq. The inserts are chromosome numbers. The borders between chromosomes are represented by vertical bars. (b) Our analysis of S1514. The normal state, where the copy number in the target agrees with that in the control, should have mean 0. A contiguous range of measurements whose average is higher or lower than 0 suggests a respective gain or loss in copy number. To identify gains and losses, we used τ+ = 0.3 and τ− = −0.3, respectively. We found single-copy duplication from the center to the end of chromosome 3. We identified double-copy duplication at the beginning of chromosome 5 and single-copy duplication in the remaining region of chromosome 5. We also identified very high-level amplification from the center to the end of chromosome 20. We found low-level losses on chromosome 13. The red lines indicate the mean values among the probes in segments detected by our method.