[BioC] Is it okay to do 2 loess normalizations in a row?

[Richard Friedman]

Dear Bioconductor Users,

	Long time readers of this column realize that I have been experiencing 
some difficulty
flattening the M vs A curve on my normalization. I have just tried 
applying 2 loess normalizations in a row with the default. That is to 
say I have done:

ira.norm <- maNorm(ira.raw, norm = "p")

ira.x2.norm <- maNorm(ira.norm, norm = "p")

	The curves flattened considerably. Is there a potenial problem with 
this procedure?

Thanks and best wishes,
Rich
------------------------------------------------------------
Richard A. Friedman, PhD
Associate Research Scientist
Herbert Irving Comprehensive Cancer Center
Oncoinformatics Core
Lecturer
Department of Biomedical Informatics
Box 95, Room 130BB or P&S 1-420C
Columbia University Medical Center
630 W. 168th St.
New York, NY 10032
(212)305-6901 (5-6901) (voice)
friedman at cancercenter.columbia.edu
http://cancercenter.columbia.edu/~friedman/


"Spring, Summer, and Winter.
Then Fall came along,
and that's the end of our song,
and the pigeons never hibernate at all".
-Rose Friedman, age 7
(These are the correct lyrics and supersede
the version previously at the end of my sig)