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• Gene symbols display parallel to chromosome regions on the matrix.
• Sample ID column headings display the Subject ID/Sample ID (for example, E09262/E09262) because each calculation is based on a comparison of a tumor and matched blood sample from the same subject.
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  The values in the Sample ID columns are mean segment values as calculated by the DNAcopy algorithm, shown in the following figure. These are expressed as log2 (test/reference, as in tumor/normal). For more information about the algorithm, see Bioconductor

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  DNAcopy ouput values can be negative. If the test and the reference genomic samples both have two copies of a chromosomal region, the ratio of test/reference is '1', and the log2(1) = 0. That is, if there is no change in the chromosomal structure, then the value is 0. If there are more copies in the test sample (amplification of the chromosomal segment), the ratio of test to reference is greater than 1, and the log2(test/reference) is greater than 0. For example, if the test sample has 6, the ratio or test/reference is 6/2 = 3; log2(3) = 1.58. In a deletion, the test is less than the reference, for example 1. The DNAcopy output value would be log2(1/2) = log2(0.5) = -1.0. Values below -0.6 are often considered a deletion.

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