[BioC] VSN, RMA, dCHIP, etc....

[Stefan Thomsen]

Dear all, 

currently evaluating the performance of different normalization strategies 
to an Affymetrix data set, I have some semi-technical, semi-philosophical 
questions.

Given (i) the jungle of possible normalization strategies implemented in R 
and other platforms, (ii) the fact that most authors describe which 
normalization strategy they used but not why they chose this and no other, 
(iii) the sparse literature on how to find the strategy most suitable for a 
given design/experiment/data set, I would be very grateful for any comments 
on the following questions:

1) Are there written or silently accepted guidelines to evaluate, choose, 
and justify the choice of normalization strategies?

2) What could be sensible "readouts" for the performance of a given 
normalization strategy ? (Personally, I am looking at the performance on 
spike-in-control and a handful of known gene profiles. I am very intersted 
in complementary approaches)

3) Is there some literature on this issue that may have escaped my notice?


Any comments on this issue would be highly appreciated.

Kind regards,

Stefan

-- 
Dr. Stefan Thomsen
Research Associate

Department of Zoology
University of Cambridge
Downing Street
Cambridge CB2 3EJ

Tel.: +44 1223 336623 
Fax:  +44 1223 336679

stt26 at cam.ac.uk