[BioC] Terminology was RE: RMA normalization

[w.huber at dkfz-heidelberg.de]

Hi Ben,

> I hate to be pedantic, but really people should be careful about how
> they utilize the term "normalization".  ...

I fully agree with your posting, I didn't intend to equate RMA or GCRMA
with just normalization and I had hoped that everybody on this list was
aware that Affymetrix preprocessing involves more than just
"normalization". But these other aspects weren't the point of our posting,
which equally applies to vsn, loess, whatever.

In fact I think "normalization" is not a very useful term at all: what we
do there has nothing to do with the normal distribution, and I don't see
what meaning the word root "normal" has in there.

The word is often used in muddled way to mean all sorts of pre-processing.
But again, "pre-processing" is not a particularly precise or intuitive
term either.

The problem I see is that the different aspects of pre-processing are not
independent of each other; as soon as you start slicing up the problem of
pre-processing in different sub-steps, that already involves
approximations and presumptions about how to solve the problem. In the
affy package / expresso method you (and Rafa & Laurent & others) have come
up with a great and extremely useful way of slicing up the problem, but of
course that's not the end of the story (as I understand, does the
continuing work on methods like affyPLM indicate.)

Best wishes
 Wolfgang