Hello All!

I am hoping that someone might have some suggestions for a normalization 
method when some of the samples in an experiment are very divergent due to 
biology, not artifact.
I have tried out several (loess, rma, vsn, quantile) but I am worried by 
how similar the distributions look afterwards.
It would be best to use a set of 'housekeeping genes'?  The normal ones 
(rRNA, gapdh, actin, etc) all are biologically different in these 
treatments too (think dying tissue).
Formally we were using mas5 type summarization......but since it isn't the 
most robust I wanted to try some other methods out.  Is the mas5 type of 
constant normalization really the best for this type of data and I am 
chasing my tail?

Thanks for any advice!
Siobhan

S. A. Braybrook
Graduate Student, Harada Lab
Section of Plant Biology
University of California,  Davis
Davis, CA 95616
Ph 530.752.6980

The time is always right, to do what is right.
- Martin Luther King, Jr.  
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