[BioC] Difficulty in getting a boxplot display of nomralized datausing affy

James MacDonald jmacdon at med.umich.edu
Thu Apr 29 22:08:01 CEST 2004

I don't think there is a boxplot command for an exprSet. You could try




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> 04/29/04
03:47PM >>>
Dear Bioconductor users,

	I am currently running the latest version of affy 1.4.22 under
R 1.9.0 on Mac OSX 10.3. I am able to get a boxplot on the unnormalized

but not on the normalized data. Here are excerpts from my session:
 > howard1.raw
AffyBatch object
size of arrays=640x640 features (67206 kb)
cdf=MG_U74Av2 (12488 affyids)
number of samples=21
number of genes=12488

 > howard1.norm <- rma(howard1.raw)
 > howard1.norm
Expression Set (exprSet) with
	12488 genes
	21 samples
		 phenoData object with 1 variables and 21 cases
		sample: arbitrary numbering
 > boxplot(howard1.raw)
Yielded a boxplot.
 > boxplot(howard1.norm)
Error in boxplot.default(howard1.norm) : invalid first argument

Question: Should the rma normalized file be displayed by boxplot with 
commands that I have typed?
If not: Is there a way to display a boxplot of the normalized file?
If so: any suggestions.
In addition to affy, I so far have the following packages installed in

my Library:
[bb01friedman1:~/Library/R/library] friedman% ls
Biobase         R.css           affy            affyPLM         
affycomp        liblisting.Rda  mgu74av2cdf     reposTools

Do I need anything else to run box plot on the normalized object?

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 

"'Chutes and Ladders' teaches cause and effect." - Rose Friedman, age

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