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TCGA-copy-number.md

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Segment_Mean is the log2 ratio of the sample (tumor and matched normal) intensity to the reference pool intensity. 0 means the CN is 2N. To convert to an absolute cn, use: (2^seg_mean)*2 see here

In general a zero value corresponding to CN2. You have to define a threshold for a deletion and duplication. This group used -0.2 and 0.2, respectively. http://mcr.aacrjournals.org/content/12/4/485.long