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

[Richard Friedman]

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 
data
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
annotation=mgu74av2

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

Question: Should the rma normalized file be displayed by boxplot with 
the
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,
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/

"'Chutes and Ladders' teaches cause and effect." - Rose Friedman, age 7
-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Type: text/enriched
Size: 2149 bytes
Desc: not available
Url : https://www.stat.math.ethz.ch/pipermail/bioconductor/attachments/20040429/929699f4/attachment.bin