vsn: meanSdPlot + MAlist
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Guido Hooiveld ★ 3.0k
@guido-hooiveld-2020
Last seen 2 days ago
Wageningen University, Wageningen, the …
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_NAM E= C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICA TI 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 [[alternative HTML version deleted]]
Normalization vsn limma convert Normalization vsn limma convert • 1.5k views
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@martin-morgan-1513
Last seen 22 days ago
United States
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_N AME= > C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFI CATI > 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
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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_IDENTIF ICATI >> 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
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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
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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 > ------------------------------------------------------- > >
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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
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