[BioC] Dist of exprSet object

[James W. MacDonald]

You don't really need affyPLM. The problem is that the boxplot method 
for a matrix just gives you one big box, instead of a boxplot for each 
column. However, the boxplot method for a data.frame _will_ give you a 
box for each column.

boxplot(as.data.frame(exprs(eset)))

Best,

Jim


Ben Bolstad wrote:
> 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
>>
>>
>>______________________________________________________
>>
>>The contents of this e-mail are privileged and/or confidenti...{{dropped}}
>>
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> 
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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