[BioC] RE: quantile normalization

[H. Han]

----- Original Message ----- 
From: "Remo Sanges" <sanges at biogem.it>
> There are more changed genes when you normalize within tissue-of-origin
> instead of rma(cel.data). Now the problem is to understand if this
> variability
> is due to numerical of biological issue.

I believe we can explain more changed genes by assumption changes. In
all-sample normalization, we assume on average gene does not change (average
diff = 0)  whereas in the within normalization, we relaxed the assumption
(average <>0). in my case, e.g, after within group norm, i found the second
group in general expresses lower than the first. Both the number of sig
genes and direction of change (mostly repressed) are dictated by this
"average diff".

cheers,
Hillary