Question: backgroundCorrect for RGlist
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gravatar for Harpreet Saini
10.9 years ago by
United Kingdom
Harpreet Saini30 wrote:
Hi, I am analyzing the two-color array data and for the background correction, I am using the backgroundCorrect function. RGb<-backgroundCorrect(RG,method="normexp",offset=50). where RG is the RGlist. I am getting the following error: Error in function (classes, fdef, mtable) : unable to find an inherited method for function "backgroundCorrect", for signature "RGList" Here is my sessionInfo() R version 2.8.0 (2008-10-20) i386-apple-darwin8.11.1 locale: C attached base packages: [1] grid splines tools stats graphics grDevices utils [8] datasets methods base other attached packages: [1] statmod_1.3.8 MASS_7.2-45 [3] Ringo_1.6.0 SparseM_0.78 [5] arrayQualityMetrics_1.8.1 marray_1.20.0 [7] beadarray_1.10.0 sma_0.5.15 [9] hwriter_0.93 latticeExtra_0.5-4 [11] simpleaffy_2.18.0 affyPLM_1.18.0 [13] preprocessCore_1.4.0 gcrma_2.14.1 [15] matchprobes_1.14.1 RColorBrewer_1.0-2 [17] vsn_3.8.0 affy_1.20.0 [19] genefilter_1.22.0 survival_2.34-1 [21] geneplotter_1.20.0 annotate_1.20.1 [23] xtable_1.5-4 AnnotationDbi_1.4.2 [25] lattice_0.17-17 Biobase_2.2.1 [27] limma_2.16.3 loaded via a namespace (and not attached): [1] DBI_0.2-4 KernSmooth_2.22-22 RSQLite_0.7-1 affyio_1.10.1 -- Any help would be great. Thanks. Harpreet Kaur Saini Enright Group EMBL - European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD Tel: +44-(0)-1223-492676
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ADD COMMENTlink modified 10.9 years ago by Wolfgang Huber13k • written 10.9 years ago by Harpreet Saini30
Answer: backgroundCorrect for RGlist
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gravatar for Wolfgang Huber
10.9 years ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:
Dear Harpreet the "beadarray" and the "limma" package both define generic functions "backgroundCorrect", and according to your sessionInfo "beadarray" comes earlier in your search path. When you load "beadarray", do you also get (as I do): The following object(s) are masked from package:limma : backgroundCorrect, imageplot, plotMA As a solution for your problem, you can always call the version of backgroundCorrect that you mean by qualifying it with: limma::backgroundCorrect And you can check whether you really need to attach "beadarray" for your analysis. In general, there is no guarantee with R that different user- contributed packages do not define the same symbols - hence learning to work with namespaces is a good thing for developers, as well as for users. Best wishes Wolfgang Wolfgang Huber, EBI Harpreet Kaur Saini ha scritto: > Hi, > > I am analyzing the two-color array data and for the background correction, > I am using the backgroundCorrect function. > > RGb<-backgroundCorrect(RG,method="normexp",offset=50). > > where RG is the RGlist. > > I am getting the following error: > > Error in function (classes, fdef, mtable) : > unable to find an inherited method for function "backgroundCorrect", for > signature "RGList" > > Here is my sessionInfo() > R version 2.8.0 (2008-10-20) > i386-apple-darwin8.11.1 > > locale: > C > > attached base packages: > [1] grid splines tools stats graphics grDevices utils > [8] datasets methods base > > other attached packages: > [1] statmod_1.3.8 MASS_7.2-45 > [3] Ringo_1.6.0 SparseM_0.78 > [5] arrayQualityMetrics_1.8.1 marray_1.20.0 > [7] beadarray_1.10.0 sma_0.5.15 > [9] hwriter_0.93 latticeExtra_0.5-4 > [11] simpleaffy_2.18.0 affyPLM_1.18.0 > [13] preprocessCore_1.4.0 gcrma_2.14.1 > [15] matchprobes_1.14.1 RColorBrewer_1.0-2 > [17] vsn_3.8.0 affy_1.20.0 > [19] genefilter_1.22.0 survival_2.34-1 > [21] geneplotter_1.20.0 annotate_1.20.1 > [23] xtable_1.5-4 AnnotationDbi_1.4.2 > [25] lattice_0.17-17 Biobase_2.2.1 > [27] limma_2.16.3 > > loaded via a namespace (and not attached): > [1] DBI_0.2-4 KernSmooth_2.22-22 RSQLite_0.7-1 affyio_1.10.1
ADD COMMENTlink written 10.9 years ago by Wolfgang Huber13k
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