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

[Richard Friedman]

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 
Speed

does the program normalize

log(M) vs A

or

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

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.
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