[BioC] Aquantile normalization & transcriptional activity

[Federico Scossa]

Hi all,

I have a concern about using Aquantile normalization (limma) in my 
experiment. I hope someone can help me and clarify the issue.... I have 
several timepoints... in particular one of them, as expected, shows a 
global, low trascriptional activity (the tissue at this timepoint is close 
to the "drying stage", so most of the genes are not expressed)...
so if I apply Aquantile normalization I am going to modify the channel 
densities, so that they can overlap. and this is necessary, as far as I 
understand, because it makes the between-timepoints comparisons possible 
(my design is unconnected). but, in this way, am I introducing some 
artifacts in my low-expression timepoints? I mean, I am forcing  the 
channel intensities to have all the same distribution... but which is the 
assumption of Aquantile ? should the single channel intensities be roughly 
the same before normalization?

thank you ! any help welcome !

Federico