[BioC] vsn: meanSdPlot + MAlist

[Martin Morgan]

Hi Guido --

Hooiveld, Guido wrote:
> Hi,
> I would appreciate some advice.
>  
> I am analyzing 2 color data (Agilent) using limma. Within limma I
> applied VSN normalization. So far, so good. 
> Now i would like to use the 'meanSdPlot' function to 'verify the fit'
> (as is strongly recommended after running vsn). However, this function
> meanSdPlot does not accept an object of class MAlist..., according to
> the help page only when the class of the object is a matrix,
> ExpressionSet or vsn.
>  
> Question: how to convert a MAlist into e.g. a matrix, so it can be as
> input for the function meanSdPlot?

if maList is an object of class MAList

library(convert)
as(maList, "ExpressionSet")

or simply

maList$M

Martin

>  
> Thanks,
> Guido
>  
>  
>  
>  
>> library("limma")
>> targets <- readTargets("targets.txt", row.names="Name")
>> RG <- read.maimages(targets$FileName, source="agilent")
> <<snip>>
>  
>> show(RG)
> An object of class "RGList"
> <<snip>>
>  
>> MA.vsn <- normalizeBetweenArrays(RG, method="vsn")
> Loading required package: vsn
> Loading required package: Biobase
>  
> vsn2: 45220 x 30 matrix (1 stratum). 
> Please use 'meanSdPlot' to verify the fit.    <<<--------
> 
>> meanSdPlot(MA.vsn)
> Error in function (classes, fdef, mtable)  : 
>   unable to find an inherited method for function "meanSdPlot", for
> signature "MAList"
>> class(MA.vsn)
> [1] "MAList"
> attr(,"package")
> [1] "limma"
> 
>> sessionInfo()
> R version 2.9.0 (2009-04-17) 
> x86_64-unknown-linux-gnu 
>  
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.U
> TF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=
> C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATI
> ON=C
>  
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
>  
> other attached packages:
> [1] statmod_1.4.0 vsn_3.12.0    Biobase_2.4.1 limma_2.18.2 
>  
> loaded via a namespace (and not attached):
> [1] affy_1.22.1          affyio_1.12.0        grid_2.9.0          
> [4] lattice_0.17-25      preprocessCore_1.6.0
>  
>  
> 
> ------------------------------------------------ 
> Guido Hooiveld, PhD 
> Nutrition, Metabolism & Genomics Group 
> Division of Human Nutrition 
> Wageningen University 
> Biotechnion, Bomenweg 2 
> NL-6703 HD Wageningen 
> the Netherlands 
> tel: (+)31 317 485788 
> fax: (+)31 317 483342 
> internet:   http://nutrigene.4t.com <http://nutrigene.4t.com/>  
> email:      guido.hooiveld at wur.nl 
> 
> 
> 
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> 
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

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