NKI dataset, SIRAC results of Step 1 and 2 for the different cancer subtypes. Results of Step 1 and 2 of the SIRAC algorithm for the four different subtypes in the NKI dataset. In the top panel of each figure the relevant DNA-probes detected by the SAM analysis are displayed on their genomic location (horizontal axis). For each relevant DNA-probe two circles are plotted at its location, representing the median of the class of interest (Basal, ERBB2, Luminal A or Luminal B) and the median of the remaining samples. In the bottom plot, the regions identified by the algorithm as significantly aberrated are shown for all genomic locations (horizontal axis) with a line for each window width used (vertical axis). The length of the line indicates the region on the genome that is significantly enriched with relevant DNA-probes. The color indicated whether the aberration is an amplification (green) or a deletion (red) in the class of interest, or an aberration in the other samples (gray).