[BioC] plotDeg in affycoretools

[claire wilson]

Hi Jim,

Many thanks for your prompt reply. I have used the affystart function to
load the data into R. How do I access the raw data and not just the
expression set. I would like to see the degradation and density plots,
but only the PCA one remained.

Kind Regards

Claire 

> -----Original Message-----
> From: James W. MacDonald [mailto:jmacdon at med.umich.edu] 
> Sent: 22 March 2007 13:53
> To: claire wilson
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] plotDeg in affycoretools
> 
> Hi Claire,
> 
> claire wilson wrote:
> > Hi all,
> >  
> > am getting the following error when I call plotDeg from 
> affycoretools, 
> > can anyone help me out?
> 
> It would appear that you are calling plotDeg() on an exprSet, 
> rather than an AffyBatch. At the exprSet stage you have 
> already computed expression values, so there are no longer 
> any pm probes to plot.
> 
> Best,
> 
> Jim
> 
> 
> >  
> > Many thanks
> >  
> > claire
> >  
> > 
> >>plotDeg(eset.f)
> > 
> > Error in function (classes, fdef, mtable)  : 
> >         unable to find an inherited method for function "pm", for 
> > signature "exprSet"
> > 
> >  
> > sessionInfo()
> > R version 2.4.1 (2006-12-18)
> > i386-pc-mingw32
> >  
> > locale:
> > LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
> > Kingdom.1252;LC_MONETARY=English_United
> > Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252
> >  
> > attached base packages:
> > [1] "splines"   "tools"     "stats"     "graphics"  
> "grDevices" "utils"
> > "datasets" 
> > [8] "methods"   "base"     
> >  
> > other attached packages:
> > hgu133plus2cdf  affycoretools        biomaRt          RCurl
> > XML 
> >       "1.14.0"        "1.6.1"        "1.8.2"        "0.8-0"
> > "1.6-0" 
> >        GOstats       Category     genefilter       survival
> > KEGG 
> >        "2.0.4"        "2.0.3"       "1.12.0"         "2.30"
> > "1.14.1" 
> >           RBGL       annotate             GO          graph
> > limma 
> >       "1.10.0"       "1.12.1"       "1.14.1"       "1.12.1"
> > "2.9.13" 
> >           affy         affyio        Biobase 
> >       "1.12.2"        "1.2.0"       "1.12.2" 
> > 
> > 
> > 
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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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