The segment_mean in copy number variation data of TCGA describe the log-transform copy number value of specific chromosome segment. I want to know how to pick the threshold to select abnormal fragments?
Sorry for the late reply but I hope it may help others.
In general or as per the TCGA site, a zero value corresponding to no change, while a positive value is an amplification and a negative value is a delation. Yes, you can use level 3 CNV data directly and apply your own statistical method, or can also opt for GISTIC2 to save time. This paper used -0.2 and 0.2 to consider deletion and duplication, respectively. http://mcr.aacrjournals.org/content/12/4/485.long