egdeR troubles under new R 3.02
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@alogmail2aolcom-4540
Last seen 9.9 years ago
Dear All, It seems edgeR has a bug under new R 3.0.2. Here is the example from LIMMA's guide for R-seq (p.111- etc): library(tweeDEseqCountData) > data(pickrell1) > Counts <- exprs(pickrell1.eset) > class(Counts) [1] "matrix" > dim(Counts) [1] 38415 69 > Counts[1:5,1:5] NA18486 NA18498 NA18499 NA18501 NA18502 ENSG00000127720 6 32 14 35 14 ENSG00000242018 20 21 24 22 16 ENSG00000224440 0 0 0 0 0 ENSG00000214453 0 0 0 0 0 ENSG00000237787 0 0 1 0 0 > barplot(colSums(Counts)*1e-6, names=1:69, ylab="Library size (millions)") > Gender <- pickrell1.eset$gender etc. It finally results in: fit$df.prior [1] 4.6 > summary(decideTests(fit)) (Intercept) Gendermale -1 292 43 0 913 17251 1 16105 16 > chrom <- fit$genes$Chr > plotMA(fit,array=2,status=chrom,values=c("X","Y"),col=c("red","blue" ),main="Male vs Female",legend="bottomright") Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘plotMA’ for signature ‘"MArrayLM"’ > abline(h=0,col="darkgrey") Error in int_abline(a = a, b = b, h = h, v = v, untf = untf, ...) : plot.new has not been called yet > Thanks Alex UC Berkeley, Molecular Toxicology Berkeley CA 94720 > sessionInfo() R version 3.0.2 (2013-09-25) Platform: i386-w64-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] tweeDEseqCountData_1.0.9 DESeq2_1.1.45 RcppArmadillo_0.3.920.1 Rcpp_0.10.5 GenomicRanges_1.13.51 XVector_0.1.4 [7] IRanges_1.19.38 DESeq_1.13.3 lattice_0.20-23 locfit_1.5-9.1 Biobase_2.21.7 BiocGenerics_0.7.5 [13] edgeR_3.3.8 limma_3.17.26 BiocInstaller_1.11.4 loaded via a namespace (and not attached): [1] annotate_1.39.0 AnnotationDbi_1.23.27 DBI_0.2-7 genefilter_1.43.0 geneplotter_1.39.05 grid_3.0.2 [7] RColorBrewer_1.0-5 RSQLite_0.11.4 splines_3.0.2 stats4_3.0.2 survival_2.37-4 tools_3.0.2 [13] XML_3.98-1.1 xtable_1.7-1 [[alternative HTML version deleted]]
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@james-w-macdonald-5106
Last seen 11 hours ago
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Hi Alex, On Tuesday, October 08, 2013 10:42:33 PM, alogmail2 at aol.com wrote: > Dear All, > > > It seems edgeR has a bug under new R 3.0.2. > > > Here is the example from LIMMA's guide for R-seq (p.111- etc): > > > > library(tweeDEseqCountData) >> data(pickrell1) >> Counts <- exprs(pickrell1.eset) >> class(Counts) > [1] "matrix" >> dim(Counts) > [1] 38415 69 >> Counts[1:5,1:5] > NA18486 NA18498 NA18499 NA18501 NA18502 > ENSG00000127720 6 32 14 35 14 > ENSG00000242018 20 21 24 22 16 > ENSG00000224440 0 0 0 0 0 > ENSG00000214453 0 0 0 0 0 > ENSG00000237787 0 0 1 0 0 >> barplot(colSums(Counts)*1e-6, names=1:69, ylab="Library size (millions)") >> Gender <- pickrell1.eset$gender > > > > etc. > > > It finally results in: > > > > fit$df.prior > [1] 4.6 >> summary(decideTests(fit)) > (Intercept) Gendermale > -1 292 43 > 0 913 17251 > 1 16105 16 >> chrom <- fit$genes$Chr >> plotMA(fit,array=2,status=chrom,values=c("X","Y"),col=c("red","blue "),main="Male vs Female",legend="bottomright") > Error in (function (classes, fdef, mtable) : > unable to find an inherited method for function ???plotMA??? for signature ???"MArrayLM"??? This is the sort of error you get when you have function masking. You loaded the limma package, which has a plotMA function, then you loaded (in an unknown order) the DESeq package, which also has a plotMA function, then you loaded DESeq2 which _also_ has a plotMA function. So when you say plotMA(<marraylm object="">), R looks down the search path and sees the plotMA function in either DESeq or DESeq2 (whichever was loaded last), looks at the methods available, and says 'this function doesn't work on that sort of object'. The work-around is to use limma::plotMA(), which tells R to look for the function in the correct package namespace. Best, Jim >> abline(h=0,col="darkgrey") > Error in int_abline(a = a, b = b, h = h, v = v, untf = untf, ...) : > plot.new has not been called yet >> > > > Thanks > > > Alex > > > UC Berkeley, Molecular Toxicology > Berkeley CA 94720 > > > > >> sessionInfo() > R version 3.0.2 (2013-09-25) > Platform: i386-w64-mingw32/i386 (32-bit) > > > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C LC_TIME=English_United States.1252 > > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods base > > > other attached packages: > [1] tweeDEseqCountData_1.0.9 DESeq2_1.1.45 RcppArmadillo_0.3.920.1 Rcpp_0.10.5 GenomicRanges_1.13.51 XVector_0.1.4 > [7] IRanges_1.19.38 DESeq_1.13.3 lattice_0.20-23 locfit_1.5-9.1 Biobase_2.21.7 BiocGenerics_0.7.5 > [13] edgeR_3.3.8 limma_3.17.26 BiocInstaller_1.11.4 > > > loaded via a namespace (and not attached): > [1] annotate_1.39.0 AnnotationDbi_1.23.27 DBI_0.2-7 genefilter_1.43.0 geneplotter_1.39.05 grid_3.0.2 > [7] RColorBrewer_1.0-5 RSQLite_0.11.4 splines_3.0.2 stats4_3.0.2 survival_2.37-4 tools_3.0.2 > [13] XML_3.98-1.1 xtable_1.7-1 > > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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On 9 Oct 2013, at 16:55, "James W. MacDonald" <jmacdon at="" uw.edu=""> wrote: > > This is the sort of error you get when you have function masking. You loaded the limma package, which has a plotMA function, then you loaded (in an unknown order) the DESeq package, which also has a plotMA function, then you loaded DESeq2 which _also_ has a plotMA function. > In Bioc 2.13, plotMA is a generic function in BiocGenerics and various other packages define their methods for that. Best wishes Wolfgang > So when you say plotMA(<marraylm object="">), R looks down the search path and sees the plotMA function in either DESeq or DESeq2 (whichever was loaded last), looks at the methods available, and says 'this function doesn't work on that sort of object'. > > The work-around is to use limma::plotMA(), which tells R to look for the function in the correct package namespace. > > Best, > > Jim > > >>> abline(h=0,col="darkgrey") >> Error in int_abline(a = a, b = b, h = h, v = v, untf = untf, ...) : >> plot.new has not been called yet >>> >> >> >> Thanks >> >> >> Alex >> >> >> UC Berkeley, Molecular Toxicology >> Berkeley CA 94720 >> >> >> >> >>> sessionInfo() >> R version 3.0.2 (2013-09-25) >> Platform: i386-w64-mingw32/i386 (32-bit) >> >> >> locale: >> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 >> [4] LC_NUMERIC=C LC_TIME=English_United States.1252 >> >> >> attached base packages: >> [1] parallel stats graphics grDevices utils datasets methods base >> >> >> other attached packages: >> [1] tweeDEseqCountData_1.0.9 DESeq2_1.1.45 RcppArmadillo_0.3.920.1 Rcpp_0.10.5 GenomicRanges_1.13.51 XVector_0.1.4 >> [7] IRanges_1.19.38 DESeq_1.13.3 lattice_0.20-23 locfit_1.5-9.1 Biobase_2.21.7 BiocGenerics_0.7.5 >> [13] edgeR_3.3.8 limma_3.17.26 BiocInstaller_1.11.4 >> >> >> loaded via a namespace (and not attached): >> [1] annotate_1.39.0 AnnotationDbi_1.23.27 DBI_0.2-7 genefilter_1.43.0 geneplotter_1.39.05 grid_3.0.2 >> [7] RColorBrewer_1.0-5 RSQLite_0.11.4 splines_3.0.2 stats4_3.0.2 survival_2.37-4 tools_3.0.2 >> [13] XML_3.98-1.1 xtable_1.7-1 >> >> >> >> >> [[alternative HTML version deleted]] >> >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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On Wednesday, October 09, 2013 10:59:24 AM, Wolfgang Huber wrote: > > On 9 Oct 2013, at 16:55, "James W. MacDonald" <jmacdon at="" uw.edu=""> wrote: >> >> This is the sort of error you get when you have function masking. You loaded the limma package, which has a plotMA function, then you loaded (in an unknown order) the DESeq package, which also has a plotMA function, then you loaded DESeq2 which _also_ has a plotMA function. >> > > In Bioc 2.13, plotMA is a generic function in BiocGenerics and various other packages define their methods for that. And that might actually matter if limma used S4 methods. But it does not, so the existence of a generic in this instance is irrelevant. Best, Jim > > Best wishes > Wolfgang > >> So when you say plotMA(<marraylm object="">), R looks down the search path and sees the plotMA function in either DESeq or DESeq2 (whichever was loaded last), looks at the methods available, and says 'this function doesn't work on that sort of object'. >> >> The work-around is to use limma::plotMA(), which tells R to look for the function in the correct package namespace. >> >> Best, >> >> Jim >> >> >>>> abline(h=0,col="darkgrey") >>> Error in int_abline(a = a, b = b, h = h, v = v, untf = untf, ...) : >>> plot.new has not been called yet >>>> >>> >>> >>> Thanks >>> >>> >>> Alex >>> >>> >>> UC Berkeley, Molecular Toxicology >>> Berkeley CA 94720 >>> >>> >>> >>> >>>> sessionInfo() >>> R version 3.0.2 (2013-09-25) >>> Platform: i386-w64-mingw32/i386 (32-bit) >>> >>> >>> locale: >>> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 >>> [4] LC_NUMERIC=C LC_TIME=English_United States.1252 >>> >>> >>> attached base packages: >>> [1] parallel stats graphics grDevices utils datasets methods base >>> >>> >>> other attached packages: >>> [1] tweeDEseqCountData_1.0.9 DESeq2_1.1.45 RcppArmadillo_0.3.920.1 Rcpp_0.10.5 GenomicRanges_1.13.51 XVector_0.1.4 >>> [7] IRanges_1.19.38 DESeq_1.13.3 lattice_0.20-23 locfit_1.5-9.1 Biobase_2.21.7 BiocGenerics_0.7.5 >>> [13] edgeR_3.3.8 limma_3.17.26 BiocInstaller_1.11.4 >>> >>> >>> loaded via a namespace (and not attached): >>> [1] annotate_1.39.0 AnnotationDbi_1.23.27 DBI_0.2-7 genefilter_1.43.0 geneplotter_1.39.05 grid_3.0.2 >>> [7] RColorBrewer_1.0-5 RSQLite_0.11.4 splines_3.0.2 stats4_3.0.2 survival_2.37-4 tools_3.0.2 >>> [13] XML_3.98-1.1 xtable_1.7-1 >>> >>> >>> >>> >>> [[alternative HTML version deleted]] >>> >>> >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> -- >> James W. MacDonald, M.S. >> Biostatistician >> University of Washington >> Environmental and Occupational Health Sciences >> 4225 Roosevelt Way NE, # 100 >> Seattle WA 98105-6099 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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On 9 Oct 2013, at 17:04, James W. MacDonald <jmacdon at="" uw.edu=""> wrote: > On Wednesday, October 09, 2013 10:59:24 AM, Wolfgang Huber wrote: >> On 9 Oct 2013, at 16:55, "James W. MacDonald" <jmacdon at="" uw.edu=""> wrote: >>> >>> This is the sort of error you get when you have function masking. You loaded the limma package, which has a plotMA function, then you loaded (in an unknown order) the DESeq package, which also has a plotMA function, then you loaded DESeq2 which _also_ has a plotMA function. >>> >> >> In Bioc 2.13, plotMA is a generic function in BiocGenerics and various other packages define their methods for that. > > And that might actually matter if limma used S4 methods. But it does not, so the existence of a generic in this instance is irrelevant. This design decision is up to the package maintainer, but the effort of wrapping a "normal" function into a method that is also registered with BiocGenerics::plotMA would be quite minimal (and not preclude being able to still call the normal function directly, as always.) The concept of a project-wide common name space is probably elusive and ultimately misguided, but some approximation for the most popular name choices is what BiocGenerics attempts. Kind regards Wolfgang > Best, > > Jim > > >> >> Best wishes >> Wolfgang >> >>> So when you say plotMA(<marraylm object="">), R looks down the search path and sees the plotMA function in either DESeq or DESeq2 (whichever was loaded last), looks at the methods available, and says 'this function doesn't work on that sort of object'. >>> >>> The work-around is to use limma::plotMA(), which tells R to look for the function in the correct package namespace. >>> >>> Best, >>> >>> Jim >>> >>> >>>>> abline(h=0,col="darkgrey") >>>> Error in int_abline(a = a, b = b, h = h, v = v, untf = untf, ...) : >>>> plot.new has not been called yet >>>>> >>>> >>>> >>>> Thanks >>>> >>>> >>>> Alex >>>> >>>> >>>> UC Berkeley, Molecular Toxicology >>>> Berkeley CA 94720 >>>> >>>> >>>> >>>> >>>>> sessionInfo() >>>> R version 3.0.2 (2013-09-25) >>>> Platform: i386-w64-mingw32/i386 (32-bit) >>>> >>>> >>>> locale: >>>> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 >>>> [4] LC_NUMERIC=C LC_TIME=English_United States.1252 >>>> >>>> >>>> attached base packages: >>>> [1] parallel stats graphics grDevices utils datasets methods base >>>> >>>> >>>> other attached packages: >>>> [1] tweeDEseqCountData_1.0.9 DESeq2_1.1.45 RcppArmadillo_0.3.920.1 Rcpp_0.10.5 GenomicRanges_1.13.51 XVector_0.1.4 >>>> [7] IRanges_1.19.38 DESeq_1.13.3 lattice_0.20-23 locfit_1.5-9.1 Biobase_2.21.7 BiocGenerics_0.7.5 >>>> [13] edgeR_3.3.8 limma_3.17.26 BiocInstaller_1.11.4 >>>> >>>> >>>> loaded via a namespace (and not attached): >>>> [1] annotate_1.39.0 AnnotationDbi_1.23.27 DBI_0.2-7 genefilter_1.43.0 geneplotter_1.39.05 grid_3.0.2 >>>> [7] RColorBrewer_1.0-5 RSQLite_0.11.4 splines_3.0.2 stats4_3.0.2 survival_2.37-4 tools_3.0.2 >>>> [13] XML_3.98-1.1 xtable_1.7-1 >>>> >>>> >>>> >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> -- >>> James W. MacDonald, M.S. >>> Biostatistician >>> University of Washington >>> Environmental and Occupational Health Sciences >>> 4225 Roosevelt Way NE, # 100 >>> Seattle WA 98105-6099 >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099
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@wolfgang-huber-3550
Last seen 11 weeks ago
EMBL European Molecular Biology Laborat…
Dear Alex this is because you have multiple packages in your search path that define a function "plotMA". Use the fully qualified path "limma::plotMA" to avoid the problem; alternatively, don't attach these other packages. This used to be DESeq in the last release, and it will be BiocGenerics in the next. (The latter now offers package authors the opportunity to register "plotMA" methods to that generic function, with their signature of choice, and spare users the confusion.) Kind regards Wolfgang On 9 Oct 2013, at 04:42, alogmail2 at aol.com wrote: > Dear All, > > > It seems edgeR has a bug under new R 3.0.2. > > > Here is the example from LIMMA's guide for R-seq (p.111- etc): > > > > library(tweeDEseqCountData) >> data(pickrell1) >> Counts <- exprs(pickrell1.eset) >> class(Counts) > [1] "matrix" >> dim(Counts) > [1] 38415 69 >> Counts[1:5,1:5] > NA18486 NA18498 NA18499 NA18501 NA18502 > ENSG00000127720 6 32 14 35 14 > ENSG00000242018 20 21 24 22 16 > ENSG00000224440 0 0 0 0 0 > ENSG00000214453 0 0 0 0 0 > ENSG00000237787 0 0 1 0 0 >> barplot(colSums(Counts)*1e-6, names=1:69, ylab="Library size (millions)") >> Gender <- pickrell1.eset$gender > > > > etc. > > > It finally results in: > > > > fit$df.prior > [1] 4.6 >> summary(decideTests(fit)) > (Intercept) Gendermale > -1 292 43 > 0 913 17251 > 1 16105 16 >> chrom <- fit$genes$Chr >> plotMA(fit,array=2,status=chrom,values=c("X","Y"),col=c("red","blue "),main="Male vs Female",legend="bottomright") > Error in (function (classes, fdef, mtable) : > unable to find an inherited method for function ?plotMA? for signature ?"MArrayLM"? >> abline(h=0,col="darkgrey") > Error in int_abline(a = a, b = b, h = h, v = v, untf = untf, ...) : > plot.new has not been called yet >> > > > Thanks > > > Alex > > > UC Berkeley, Molecular Toxicology > Berkeley CA 94720 > > > > >> sessionInfo() > R version 3.0.2 (2013-09-25) > Platform: i386-w64-mingw32/i386 (32-bit) > > > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C LC_TIME=English_United States.1252 > > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods base > > > other attached packages: > [1] tweeDEseqCountData_1.0.9 DESeq2_1.1.45 RcppArmadillo_0.3.920.1 Rcpp_0.10.5 GenomicRanges_1.13.51 XVector_0.1.4 > [7] IRanges_1.19.38 DESeq_1.13.3 lattice_0.20-23 locfit_1.5-9.1 Biobase_2.21.7 BiocGenerics_0.7.5 > [13] edgeR_3.3.8 limma_3.17.26 BiocInstaller_1.11.4 > > > loaded via a namespace (and not attached): > [1] annotate_1.39.0 AnnotationDbi_1.23.27 DBI_0.2-7 genefilter_1.43.0 geneplotter_1.39.05 grid_3.0.2 > [7] RColorBrewer_1.0-5 RSQLite_0.11.4 splines_3.0.2 stats4_3.0.2 survival_2.37-4 tools_3.0.2 > [13] XML_3.98-1.1 xtable_1.7-1 > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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@gordon-smyth
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WEHI, Melbourne, Australia
> Date: Tue, 8 Oct 2013 22:42:33 -0400 (EDT) > From: alogmail2 at aol.com > To: bioconductor at r-project.org > Subject: [BioC] egdeR troubles under new R 3.02 > > Dear All, > > It seems edgeR has a bug under new R 3.0.2. Poor edgeR! None of the functions you use here even belong to the edgeR package. Gordon > Here is the example from LIMMA's guide for R-seq (p.111- etc): > > library(tweeDEseqCountData) >> data(pickrell1) >> Counts <- exprs(pickrell1.eset) >> class(Counts) > [1] "matrix" >> dim(Counts) > [1] 38415 69 >> Counts[1:5,1:5] > NA18486 NA18498 NA18499 NA18501 NA18502 > ENSG00000127720 6 32 14 35 14 > ENSG00000242018 20 21 24 22 16 > ENSG00000224440 0 0 0 0 0 > ENSG00000214453 0 0 0 0 0 > ENSG00000237787 0 0 1 0 0 >> barplot(colSums(Counts)*1e-6, names=1:69, ylab="Library size (millions)") >> Gender <- pickrell1.eset$gender > > etc. > > It finally results in: > > fit$df.prior > [1] 4.6 >> summary(decideTests(fit)) > (Intercept) Gendermale > -1 292 43 > 0 913 17251 > 1 16105 16 >> chrom <- fit$genes$Chr >> plotMA(fit,array=2,status=chrom,values=c("X","Y"),col=c("red","blue "),main="Male vs Female",legend="bottomright") > Error in (function (classes, fdef, mtable) : > unable to find an inherited method for function ???plotMA??? for signature ???"MArrayLM"??? >> abline(h=0,col="darkgrey") > Error in int_abline(a = a, b = b, h = h, v = v, untf = untf, ...) : > plot.new has not been called yet > > Thanks > Alex > > > UC Berkeley, Molecular Toxicology > Berkeley CA 94720 > >> sessionInfo() > R version 3.0.2 (2013-09-25) > Platform: i386-w64-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C LC_TIME=English_United States.1252 > > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods base > > > other attached packages: > [1] tweeDEseqCountData_1.0.9 DESeq2_1.1.45 RcppArmadillo_0.3.920.1 Rcpp_0.10.5 GenomicRanges_1.13.51 XVector_0.1.4 > [7] IRanges_1.19.38 DESeq_1.13.3 lattice_0.20-23 locfit_1.5-9.1 Biobase_2.21.7 BiocGenerics_0.7.5 > [13] edgeR_3.3.8 limma_3.17.26 BiocInstaller_1.11.4 > > > loaded via a namespace (and not attached): > [1] annotate_1.39.0 AnnotationDbi_1.23.27 DBI_0.2-7 genefilter_1.43.0 geneplotter_1.39.05 grid_3.0.2 > [7] RColorBrewer_1.0-5 RSQLite_0.11.4 splines_3.0.2 stats4_3.0.2 survival_2.37-4 tools_3.0.2 > [13] XML_3.98-1.1 xtable_1.7-1 ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:5}}
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