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

[Julia Engelmann]

Hi Richard,

for me it works with:

> boxplot(data.frame(exprs(howard1.norm)), 
names=c("Exp1","Exp2","Exp3","Exp4"))

Note that if you want to use the "names" argument you must specify a name for 
each array (4 in my example ).

Hope that helps,
Julia


On Thursday 29 April 2004 21:47, Richard Friedman wrote:
> 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