[BioC] Question on normalization

[Rafael A. Irizarry]

i dont know about a concensus but... if you look at how different
replicate arrays can be (see Figure 2 here
http://www.biostat.jhsph.edu/~ririzarr/papers/affy1.pdf), it seems
impossible to argue that over-all differences in intensities are due to
biological variation as opposed to obsucuring variation. to me, this
means that in general, we are left with no choice but to assume that,
over-all, genes behave similarly across conditions and normalize
everything together. an alternative would
be to use control genes, but past attempts seemed to have failed.

On Mon, 17 Feb 2003, Gordon Barr wrote:

> To Bioconductor
> 
> We have used the quantile normalization method in Bioconductor and would
> like to know if there is consensus (or if not what are the opinions) about
> whether or not to normalize all experimental conditions and controls
> together or to analyze each group separately. We have two experimental
> groups and one control with multiple replicates for each from different
> animals.  The three conditions were run at the same time for each replicate
> to minimize variability between groups. It seems to us that if we normalize
> both experimental groups and controls together we will bias the results
> against ourselves, even if most gene expression levels are unchanged.
> 
> Thanks
> 
> 
> Gordon 
> 
> 
> 
> Gordon A. Barr, Ph.D.
> Professor Of Psychology
> Hunter College, CUNY
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> New York, New York 10021
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> 
> Senior Research Scientist
> Developmental Psychobiology
> NYS Psychiatric Institute
> Columbia College of Physicians and Surgeons
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