I have two questions regarding cn.mops for CNV detection.
If I would like to analyze tumor sample of different stages, should I normalize all stages together or stage-wise, when comparing to normal tissue.
For CNV detection must there be a median/mean calculation over samples or is cn.mops able to handle mutiple samples, like
referencecn.mops(rowmeans(X[,1:10]), rowmeans(X[,11:19]), ...
referencecn.mops(X[,1:10], X[,11:19], ... ad what happens here ? What is calculated for the samples in the first and second range?