[BioC] Dist of exprSet object

[Ben Bolstad]

Actually you need affyPLM loaded to boxplot an exprSet. affy only
provides the method for AffyBatch objects. Otherwise your example is
correct.

Best,

Ben	


eg .....

> library(affy)
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor


    Vignettes contain introductory material.

    To view, simply type 'openVignette()' or start with 'help(Biobase)'.

    For details on reading vignettes, see the openVignette help page.


Loading required package: affyio
> library(affydata)
> data(Dilution)
> eset <- rma(Dilution)
Background correcting
Normalizing
Calculating Expression
> boxplot(eset) # throws error
Error in boxplot.default(eset) : invalid first argument
> library(affyPLM)
Loading required package: gcrma
Loading required package: matchprobes
> boxplot(eset) #works fine.








On Thu, 2006-07-27 at 10:58 +1200, Marcus Davy wrote:
> P 17 of the vignette("affy").
> 
> e.g.
> 
> chipCols <- rainbow(ncol(exprs(affybatch.example)))
> boxplot(affybatch.example, col=chipCols)
> 
> Marcus
> 
> 
> On 7/27/06 10:40 AM, "Marco Blanchette" <mblanche at berkeley.edu> wrote:
> 
> > Thank you all,
> >
> > Using bioclite to download the annotation fixed the problem.
> >
> > Now, I am getting into simpler R problem. I have an exprSet object  of 4
> > arrays:
> >> eset
> > Expression Set (exprSet) with
> >         18952 genes
> >         4 samples
> >                  phenoData object with 1 variables and 4 cases
> >          varLabels
> >                 sample: arbitrary numbering
> >
> > My goal is to draw a boxplot of the 4 different samples. Surely I can do:
> >> boxplot (exprs(eset)[,1], exprs(eset)[,2], exprs(eset)[,3], exprs(eset)[,4],
> > col=c(2,3,4,5))
> >
> > But is there an easier way to do with without having to subscript each
> > individual column? [right now I have only 4 but when I will have 20, I¹ll
> > get bored quite rapidly]
> >
> > Sorry if this sounds easy, I am still learning the basics of R
> >
> > Marco
> > ______________________________
> > Marco Blanchette, Ph.D.
> >
> > mblanche at uclink.berkeley.edu
> >
> > Donald C. Rio's lab
> > Department of Molecular and Cell Biology
> > 16 Barker Hall
> > University of California
> > Berkeley, CA 94720-3204
> >
> > Tel: (510) 642-1084
> > Cell: (510) 847-0996
> > Fax: (510) 642-6062
> 
> 
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