Just use the default referencecn.mops function. Submit multiple tumor samples in the according input argument, and also multiple control samples in the according input argument. referencecn.mops will calculate an appropriate control sample and compare each tumor sample against the control.
happy new year!
I tried to use the mean values for all tumor samples and now I cannot detect any CNV's. So what would be the best solution if I want to compare multiple tumor samples to normal samples?
Is cn.mops able to handle such questions or can I only compare single samples one to one?