[BioC] vsn: meanSdPlot + MAlist

[Wolfgang Huber]

Wolfgang Huber wrote:
> 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.

This has been added to vsn_3.15.1 (in the devel branch).

	Enjoy,
	Wolfgang
> 
>     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
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at stat.math.ethz.ch
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives: 
>>> http://news.gmane.org/gmane.science.biology.informatics.conductor

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