[BioC] Print-tip Normalization of dye swap experiments using marrayNorm

Richard Friedman friedman at cancercenter.columbia.edu
Mon Feb 9 20:28:28 MET 2004

Dear Bioconductor users,

	If the marrayNorm command with the print-tip normalization option is 
used on a dye-reversed slide

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

is the normalization done on each printip of each slide separately, or 
is print-tip reversal taken
into account?

That is to say, referring to the the paper (or technical report) 
"Normalizalization for cDNA Micorarray Data" by Yang, Dudoit, Luu, and 

does the program normalize

log(M) vs A


1/2(M+M') vs 1/2(A+A')

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
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