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