Frequency plot of copy number aberrations. Copy number changes of 20 breast tumors are illustrated using the Piecewise Constant Fit (PCF) method in the CGH-Explorer program. Amplified regions are marked red and deleted regions are marked green. The proportion of calls (all samples combined, and deletions and amplifications combined) was adjusted to 12% (for details see Methods). For every platform, specific high frequency (over 50%) small amplification or deletion peaks are visible (marked by stars *). For the Agilent platform: amplifications at 3p, and 20q, deletions at 4p, twice at 5q, and 9q; for the ROMA/NimbleGen platform: amplifications at 15q and deletions at 14q; the Illumina platform shows lower frequency peaks, but picked up a unique amplification at 14q not seen by the other platforms. (Indicated with blue bars are regions, for which additional information is provided in Figure 7 and in Additional files 8, 11, and 12. Further are indicated with brown bars regions, for which additional information is in Additional files 9 and 10).