Hi,
I have got it working!
Thanks to both of you,
Guido
> -----Original Message-----
> From: Wolfgang Huber [mailto:whuber at embl.de]
> Sent: 12 November 2009 18:45
> To: Martin Morgan
> Cc: Hooiveld, Guido; bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] vsn: meanSdPlot + MAlist
>
> 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_U
> >> S.U
> >>
> TF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NA
> >> ME=
> >>
> C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFIC
> >> ATI
> >> 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
> >>
> >>
> >>
> >> [[alternative HTML version deleted]]
> >>
> >> _______________________________________________
> >> 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
> >
> >
>
>
> --
>
> Best wishes
> Wolfgang
>
> -------------------------------------------------------
> Wolfgang Huber
> EMBL
> http://www.embl.de/research/units/genome_biology/huber
> -------------------------------------------------------
>
>