[BioC] Bioconductor Digest, Vol 41, Issue 27

Sylvia.Merk at ukmuenster.de Sylvia.Merk at ukmuenster.de
Thu Jul 27 12:34:31 CEST 2006

Hi Marco,

Try this: (rmaData is an Expression-Set)

cols <- palette(rainbow(ncol(exprs(rmaData))))

boxplot(as.data.frame(exprs(rmaData)),outline=F, col=cols, main="Boxplot RMA")
#boxplot(as.data.frame(exprs(rmaData)), col=cols, main="Boxplot RMA")

To adapt the output:
?par -> Help for the parameters of par

Best regards, 


Message: 12
Date: Wed, 26 Jul 2006 15:40:29 -0700
From: Marco Blanchette <mblanche at berkeley.edu>
Subject: [BioC] Dist of exprSet object
To: "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>
Message-ID: <C0ED3D6D.2A10%mblanche at berkeley.edu>
Content-Type: text/plain

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
> eset
Expression Set (exprSet) with
        18952 genes
        4 samples
                 phenoData object with 1 variables and 4 cases
                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],

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 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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