I am planning to run an experiment involving copy number profiling of a set of mouse tumor samples. We are planning to use Affymetrix's Mouse Diversity Genotyping array.

I can see that a dedicated R package (MouseDivGeno) supports this array can provide a set of preliminary calls (del/neutral/amp), as well as providing input to PennCNV. Unfortunately, I cannot find estimates for the range of tumor purity (or normal contamination) that the above tools could handle. I was wondering if anyone can share their experience here.

Any thoughts/comments would be appreciated!