[BioC] RMA verse GCRMA

[Fangxin Hong]

Hi list;
I met a strange problem regarding the normalization methods,

For an experiment with 24 arrays (time order), I normalized the data by
both RMA and GCRMA. Then I tested the correlation between the normalized
data for each gene. Surprisingly, I found that about 25% genes with
correlation less than 0.7 between value normalized by RMA and GCRMA, and
only less than 50% genes have correlation >0.9. I studies the profile of
some genes, they look quite different under two methods.


Anybody met this problem before?  Which method we should trust? Any
comments/idea is appreciated. Or is it possible that I did something
wrong, I couldn't find it myself.

Thanks a lot!

Fangxin



-- 
Fangxin Hong, Ph.D.
Plant Biology Laboratory
The Salk Institute
10010 N. Torrey Pines Rd.
La Jolla, CA 92037
E-mail: fhong at salk.edu