Why is the density plot using noob normalization not smoother than Quantile normalization? Does it indicate something regarding the data? `
Why is the density plot using noob normalization not smoother than Quantile normalization? Does it indicate something regarding the data? `
It's not clear what you mean by noob normalization, since that's not actually a thing. NOOB stands for normal-exponential out-of-band background correction, and is simply a way to estimate and correct for background binding. In other words, preprocessQuantile
normalizes without background correcting first, and preprocessNoob
background corrects only. The normal workflow that uses preprocessNoob
is preprocessFunnorm
, which first background corrects, and then uses the first two principal components of the control probes to normalize the type I and II probes separately. So if you wanted to compare things, I would imagine it should be preprocessQuantile
versus preprocessFunnorm
.
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