[BioC] Display of histogram of RMA-processed data

[James MacDonald]

Try plotDensity(exprs(howard1.norm))

Jim



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623

>>> 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
command

> 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,
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/ 

"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