Hi, 

I have affy data for time and treatment, I did a two way anova for each gene. What's the correct way to evaluate whether time effect is more imporant or treatment effect is more important? I think averaging the variance component of each gene is not a very good way, since not all genes are equally important, in addition, most of the genes are noisy genes. I am thinking of doing a PCA and take the first several components, instead of doing anova on each gene, I can do two way anova on the scores of the first several component, then I can use a weighted average (weight is determined by the amount of variance each PC captured), is this a good way? Can somebody give me some suggestions on this? Thanks. 

James

       
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