Entering edit mode
Richard Friedman
★
2.0k
@richard-friedman-513
Last seen 10.2 years ago
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@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