[BioC] Display of histogram of RMA-processed data

James MacDonald jmacdon at med.umich.edu
Thu May 13 16:35:56 CEST 2004

Try plotDensity(exprs(howard1.norm))


James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

>>> Richard Friedman <friedman at cancercenter.columbia.edu> 05/13/04
10:02AM >>>
Dear Bioconductor Users,

	I wish to view the histogram of RMA processed data to
see if the RMA algorithm converged histograms of a number of slides
and got rid of a bothersome second peak. When I apply the command

 > hist(howard1.norm)
where howard1.norm is the output of the RMA command,

 > howard1.norm <-rma(howard1.raw)

I get the following errormessage:
Error in hist.default(howard1.norm) : `x' must be numeric

Jim MacDonald  pointed out to me that a file made with the

> dat1 <- normalize.AffyBatch.quantiles(dat)

can have its histogram displayed. However I want to be able to see the
histogram of dat processed by rma.

Is there any command that I can use to display the histogram of data
processed by the rma command?

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 

"I'm giving up coffee. Now that it looks like I might top
6 feet, I don't want to risk spoiling it."
- Isaac Friedman, age 14

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