[BioC] Aquantile normalization & transcriptional activity
fscossa at pw.usda.gov
Sat Mar 12 03:41:52 CET 2005
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 !
More information about the Bioconductor