[BioC] Normalization across different tissues for Affymetrix Array

[Naomi Altman]

Quantile normalization reduces the variance among the arrays 
included.  ANOVA compares the between tissue variation to the within 
tissue variation.

It is clear that Method 2 will inflate the false detection rate, by 
reduces the within tissue variation without adjusting the between 
tissue variaion.

It is not clear that Method 3 sufficiently reduces the problem 
discussed in 2, although it should "on average" (but not necessarily 
on a gene by gene basis).

I usually use Method 1, although I am sure it inflates the false 
nondetection rate.

I recommend looking at histograms of the PM probes for each array to 
see if quantile normalization across arrays make sense.  In my 
studies, the variation in the replicate samples was greater than the 
variation in samples from different tissues, so I felt comfortable 
using Method 1.

--Naomi

At 01:50 PM 5/2/2007, shirley zhang wrote:
>Dear Bioconductor:
>
>We run Affy's all exon array on 3 tissues (lung, nose, and mouth).
>For each tissue, 10 samples are in control and 10 in treatment group.
>Totally 60 samples.
>
>General speaking, the sigal from lung is similar to that of nose, and
>the signal from mouth is much lower than lung and nose.
>
>I've tried the following normalization:
>
>Method 1. Quantile Normalize all 3 tissues together
>Method 2. Quantile Normalize each tissue separately
>Method 3. Quantile Normalize each tissue separately, and then do
>Global Median aross all
>
>My question is: in order to do 2-way ANOVA including the interaction
>term between tissue and treatment, which normalization method is
>applicable?
>
>Thanks,
>
>Shirley
>
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111