I have absolute copy number data for a diploid organism. I would like to distinguish between a Gain and an Amplification. I am currently using the term Gain to define any chromosomal copy number increase from the norm - in this case 2. I would like to know if anyone has an arbitrary absolute copy number cut-off to distinguish between a Gain and and Amplification. For example, would you consider it to be a copy number greater than say copy number 4?
Well, it's amplified versus something (presumably a "normal" state/sample/etc.), so any value larger than that would be amplified. So for single-copy genes in a diploid organism, an absolute copy of 3 would be amplified. This, of course, is assuming there's no heterogeneity in whatever sample you're looking at.