I just used MutSigCV to analyze triple negative breast cancer mutation data from COSMIC. The result it gave me shows there is only one gene whose q value is less than 1.
I notice that in "Comprehensive genomic characterization of head and neck squamous cell carcinomas. Nature, 517(7536), p.576." they also used MutSigCV to analyze COSMIC data and "only 19 genes has q value less than 1".
So what's the point of using q value if nearly all genes have q value equal to 1?
Thank you all!