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What is the best way to analyse CNVs if I have multiple samples for tumor and control using the referencecn.mops function?
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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.
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Hi,
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?
Best, Danny.
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Thanks for the fast reply.
And when I want to pool the tumor data, should I calcuate the mean values for the tumors or something like this as input for the tumor in the referencecn.mops? For example referencecn.mops(rowMeans(X[,tumor]), X[,normal], ... ?
The idea is simply not to compare each tumor sample against the control instead comparing THE tumor to the control
Thanks in advance.