[BioC] vsn: meanSdPlot + MAlist

[Wolfgang Huber]

Hi Martin, Guido

it's a little bit more complicated, a correct way of doing this is:

	meanSdPlot(with(MA.vsn, cbind(A+M/2, A-M/2)))

To make this more convenient, I'll add a method with the MAList 
signature to meanSdPlot.

	Best wishes
	Wolfgang

Martin Morgan wrote:
> 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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> 
> 


-- 

Best wishes
      Wolfgang

-------------------------------------------------------
Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber