[BioC] loged data or not loged previous to use normalize.quantile

[Wolfgang Huber]

Hi Naomi,

>  While a couple of fixes 
> have been suggested (e.g. Churchill's work and MAANOVA ) these use 
> transformations that are not as readily understood as logarithms.

The simplicity of logarithms is somewhat of an illusion, though. There 
is no readily understood interpretation when the true expression of a 
gene in some of the conditions is zero (or close to zero). And there are 
many genes like that!

The only sane solution that I know of is some form of shrunken 
log-ratios (or "generalized", "moderated", however you call it). Some 
prefer to do it via transformation functions that are different from the 
logarithm function at the lower end, some more through the backdoor by 
biased background estimates (to make sure all the data stay away from 
zero), by but the end result is similar.

Best regards
   Wolfgang

-------------------------------------
Wolfgang Huber
European Bioinformatics Institute
European Molecular Biology Laboratory
Cambridge CB10 1SD
England
Phone: +44 1223 494642
Fax:   +44 1223 494486
Http:  www.ebi.ac.uk/huber