[BioC] Normalization with marray on technical replicates

[Richard Friedman]

Dear all,

	I have normalized two technical replicates
(same RNA) with marray. After normalization,
should a scatter plot of one array against another
yield a slope of 1?
I get a slope of about .5.
Does this mean that I am either something is wrong with the program,
or I am doing something wrong?
I have tried the following normalizations:

1. normp <-maNorm(raw, norm="p")
2. normg<-maNormScale(normp, norm ="g")

In each case the scatter plot yields a slope of .5 rather
than 1.

Any suggestions would be appreciated.

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/

"Little Lulu,
Reads Cthulu".
-Rose Friedman, Age 8