[BioC] plotDeg in affycoretools

[James W. MacDonald]

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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