I have downloaded a CNV file from a public database, and the platform on which the CNVs are called is Affymetrix SNP 6.0. Please take a look at the data at this link: https://docs.google.com/spreadsheets/d/10oIX-fD_kyANkbdjEf0piJxq3Nx9x5OBji1HVHrGrOo/edit#gid=0.
This is the result for a tumor-normal paired sample. don't know what tool was used to call CNVs and generate this file.
I don't have experiences handling any CNV data before, my questions are:
1. what does 'seg.mean' mean? is this an indicator of whether it's an amplification or deletion? How to tell?
2. what's listed above are all the entries in that file, so I assume these are all the CNVs identified across the genome. It seems that, for some chromosomes, i.e., chr1, the segment(s) identified are huge (chr1:61723-249224376), , does that mean, basically the whole chr1 is amplified or deleted? Can someone with much CNV experience tell me, if this kind of entry looks a valid result.