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))) Thanks Wolfgang; I woke up this morning knowing I hadn't thought it through enough! Martin > > 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=e n_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_IDENTI FICATI >>> 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 >> >> > > -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793

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 > ------------------------------------------------------- > >

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=e n_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_IDENTI FICATI >>> 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