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Old 01-11-2017, 10:09 PM   #1
Location: Sydney

Join Date: Mar 2015
Posts: 13
Default Why should MA plot be flat after normalization?

I'm talking about the slide:

In page 5, the title is "Why is Normalization an Issue?". The author compares the MA plot before and after normalization. He writes "Variation that is obscuring as opposed to interesting."

Q1: I can see the fitted red line before and after normalization. What's that red line?

Q2: Why is the second MA plot (after normalization) is better? The distribution is more symmetric, but what does that have anything to do with biological variation and statistical testing? Why should I care symmetry?

Last edited by tedwong; 01-11-2017 at 10:26 PM.
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Old 01-12-2017, 12:44 AM   #2
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

1) The expected value of the data points as a function of A.
2) We don't expect there to be a global unidirectional shift in changes, rather some genes should go up and others down.
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