Hello all,

I am looking at the Level 3 CNV files on TCGA - the ones generated using SNP microarrays. I have a few questions:

1. How is 'segment mean' calculated and what is the exact biological interpretation?
2. For each patient I have two files called e.g. `....hg19.seg.txt` and `...nocnv_hg19.seg.txt`. What does each file contain, and which should I be using?

Thanks for any help,

Stephanie
[Here][1] is the best documentation (that I know of) for TCGA SNP-array based CNV data. Regd. your two questions:

1. CBS segmentation algorithm identifies regions in the genome that, in spite of noise, probably have a uniform underlying copy number. The "segment mean" of each region is reported in the level 3 file, and can be used as the estimated CN-ratio for the segment.
2. "nocnv" just means that germline CN variations are removed. In TCGA, they ran SNP arrays on normal tissue too.

 [1]: http://software.broadinstitute.org/cancer/software/genepattern/affymetrix-snp6-copy-number-inference-pipeline