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?
 
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@wur.nl 



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