[BioC] loged data or not loged previous to use normalize.quantile
huber at ebi.ac.uk
Sun Apr 3 23:07:59 CEST 2005
> 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.
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