[BioC] Normalization across different tissues for Affymetrix Array

[shirley zhang]

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