I am working on array CGH data from a set of tumor samples with potentially high normal contamination. I have performed the necessary pre-processing (background subtraction, within array normalization) on the tumor data, and run the circular binary segmentation on the resulting log ratio values.
I have seen that people often threshold the mean segment values following this step to call gains and losses (a typical value I have seen in literature is a minimum absolute value of 0.3 for log2ratio). However, this process assumes a minimum value of tumor purity, which may not be true for a subset of my samples.
I was wondering if anyone can suggest a more systematic way of approaching this problem in presence of high level (50-80%) of normal tissue contamination in the tumor sample.