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