[R] Question about normalization to a set of internal standards

Frank E Harrell Jr f.harrell at vanderbilt.edu
Mon Mar 2 03:48:08 CET 2009

Waverley wrote:
> Hi,
> I have a question of the method as how to normalize the data sets
> according to a set of the internal measurements.
> For example, I have performed two batches of experiments contrasting
> two different conditions (positive versus negative conditions): one at
> a time.
> 1. each experiment, I measure signals of variable v1 to v100. I want
> to understand v1 to v100 change under these two contrasting conditions
> 2. Also I know different variables v101 to v1110, total of 10 of them,
> although they are different from each other, but they would of the
> same or similar values under these two contrasting conditions
> 3. How do I do the internal normalization?  How can I use the the
> variable v101 to v110 values to normalize the measures of v1 to v100
> at either positive or negative condition to minimize batch effect?  I
> hope the comparisons of values (v1 to v100) between two different
> conditions can be more accurate and robust to external noises.
> In general, I have a couple of matrices of the same dimensions and a
> reference matrix of values to be used as reference values to be
> normalize to.  How should I do that?

I don't understand your problem well, but in general internal 
normalization is by and large an attempt to avoid appropriate modeling 
(e.g., incorporating block effects or certain covariates in a regression 
model), and results in overstated confidence of the final estimates by 
not taking into account the imprecision in the normalizing factors.

Frank E Harrell Jr   Professor and Chair           School of Medicine
                      Department of Biostatistics   Vanderbilt University

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