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

Richard Friedman friedman at cancercenter.columbia.edu
Tue Feb 10 23:07:34 MET 2004

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,
Richard A. Friedman, PhD
Associate Research Scientist
Herbert Irving Comprehensive Cancer Center
Oncoinformatics Core
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

"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)

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