User: DannyM

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DannyM0
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Posts by DannyM

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cn.mops normalization of multiple samples
... Hi, I have two questions regarding cn.mops for CNV detection. 1. 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. 2. For CNV detection must there be a median/mean calculation over samples or is cn. ...
cn.mops written 3 months ago by DannyM0
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Answer: A: tumor vs control: multiple samples
... 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? ...
written 4 months ago by DannyM0
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Comment: C: tumor vs control: multiple samples
... 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 t ...
written 5 months ago by DannyM0
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tumor vs control: multiple samples
... What is the best way to analyse CNVs if I have multiple samples for tumor and control using the referencecn.mops function?   ...
cn.mops written 5 months ago by DannyM0

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