Road map of the experimental approach. We calculated the CNs from eight experiments (shown as purple box), built up a reference (mean signal intensity of Normal1 and Normal2) and determined the SNP CNAs for each sample against the reference. To assess the chromosomal segments we used the circular binary segmentation algorithm  with the restriction that adjacent SNPs with similar log2-ratios are necessary to form a segment (SNP CNAs are shown as green circles and the calculated segment segCNA is given as a red line). The SNP CNAs and segCNA values are categorized into five groups that are colored in the same manner as in Figure 3. Further, the SNP data were compared with gene expression data (given as a purple box) from the same samples.
Standfuß et al. BMC Cancer 2012 12:380 doi:10.1186/1471-2407-12-380