[BioC] Normalization with marray on technical replicates

[Jean Yee Hwa Yang]

Hi Richard,

I assume you have two technical replicate arrays and you are preforming a
scatter plot between two normalized M values. Typically, you should not
expect a correlation of 1 and you don't want to. The amount of correlation
between replicate samples M values usually depends on the number the DE
genes.  If you have very small number of DE genes you would prefer to see
very low correlation between M values.  As most of the data represents
white noise.  However, if you have a large percentage of DE genes, then
those values will drive the correlation between replicate M values and you
will observe a higher correlation.

Cheers

Jean

On Tue, 10 Aug 2004, Richard Friedman wrote:

> 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
> 
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