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Question: justRMA {affy} error
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gravatar for Julio Alejandro Di Rienzo
7.0 years ago by
Dear all I'm running R 2.13.1 and when I try to use it, I get the following error: "invalid class "AffyBath" object: undefined class for slot "experimentDAT" ("MIAxE") I used justRMA() function to read the same set of .CEL files before and I had no problem. It seems that the problem is related to new releases of R. Some advice? *The example (the working directory was previously set to the one having de .CEL files)* > library(affy) Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Mensajes de aviso perdidos 1: '.readRDS' is deprecated. Use 'readRDS' instead. See help("Deprecated") 2: '.readRDS' is deprecated. Use 'readRDS' instead. See help("Deprecated") > MEG<-justRMA() *Error en validObject(.Object) : invalid class "AffyBatch" object: undefined class for slot "experimentData" ("MIAxE") *> * > traceback()* 22: stop(msg, " ", errors, domain = NA) 21: validObject(.Object) 20: .nextMethod(.Object, ...) 19: eval(expr, envir, enclos) 18: eval(call, callEnv) 17: callNextMethod(.Object, ...) 16: .local(.Object, ...) 15: .nextMethod(.Object, assayData = assayData, phenoData = phenoData, featureData = featureData, experimentData = experimentData, annotation = annotation, protocolData = protocolData) 14: eval(expr, envir, enclos) 13: eval(call, callEnv) 12: callNextMethod(.Object, assayData = assayData, phenoData = phenoData, featureData = featureData, experimentData = experimentData, annotation = annotation, protocolData = protocolData) 11: .local(.Object, ...) 10: .nextMethod(.Object, assayData = assayData, phenoData = phenoData, featureData = featureData, experimentData = experimentData, annotation = annotation, protocolData = protocolData) 9: eval(expr, envir, enclos) 8: eval(call, callEnv) 7: callNextMethod(.Object, assayData = assayData, phenoData = phenoData, featureData = featureData, experimentData = experimentData, annotation = annotation, protocolData = protocolData) 6: .local(.Object, ...) 5: initialize(value, ...) 4: initialize(value, ...) 3: new("AffyBatch", cdfName = cdfname, annotation = cleancdfname(cdfname, addcdf = FALSE)) 2: just.rma(filenames = l$filenames, phenoData = l$phenoData, description = l$description, notes = notes, compress = compress, rm.mask = rm.mask, rm.outliers = rm.outliers, rm.extra = rm.extra, verbose = verbose, normalize = normalize, background = background, bgversion = bgversion, destructive = destructive, cdfname = cdfname) 1: justRMA() > *> sessionInfo() *R version 2.13.1 (2011-07-08) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=Spanish_Argentina.1252 LC_CTYPE=Spanish_Argentina.1252 LC_MONETARY=Spanish_Argentina.1252 [4] LC_NUMERIC=C LC_TIME=Spanish_Argentina.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] affy_1.30.0 Biobase_2.10.0 loaded via a namespace (and not attached): [1] affyio_1.20.0 preprocessCore_1.14.0 tools_2.13.1 > Prof. Julio Di Rienzo Estadística y Biometría FCA- U.N. Córdoba IBS-RARG President http://sites.google.com/site/juliodirienzo "Biometry, the active pursuit of biological knowledge by quantitative methods." (R.A. Fisher, 1948) [[alternative HTML version deleted]]
ADD COMMENTlink modified 7.0 years ago by Martin Morgan ♦♦ 22k • written 7.0 years ago by Julio Alejandro Di Rienzo10
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gravatar for Martin Morgan
7.0 years ago by
Martin Morgan ♦♦ 22k
United States
Martin Morgan ♦♦ 22k wrote:
On 08/29/2011 10:43 AM, Julio Alejandro Di Rienzo wrote: > Dear all > > I'm running R 2.13.1 and when I try to use it, I get the following > error: Hi Julio -- your version of Biobase (and perhaps other packages) is incorrect for your version of R. Update installed packages following http://bioconductor.org/install/#update-bioconductor-packages Martin > > "invalid class "AffyBath" object: undefined class for slot "experimentDAT" > ("MIAxE") > > I used justRMA() function to read the same set of .CEL files before and I > had no problem. It seems that the problem is related to new releases of R. > > Some advice? > > *The example (the working directory was previously set to the one having de > .CEL files)* > >> library(affy) > Loading required package: Biobase > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation(pkgname)'. > > Mensajes de aviso perdidos > 1: '.readRDS' is deprecated. > Use 'readRDS' instead. > See help("Deprecated") > 2: '.readRDS' is deprecated. > Use 'readRDS' instead. > See help("Deprecated") >> MEG<-justRMA() > *Error en validObject(.Object) : > invalid class "AffyBatch" object: undefined class for slot > "experimentData" ("MIAxE") > *> > * >> traceback()* > 22: stop(msg, " ", errors, domain = NA) > 21: validObject(.Object) > 20: .nextMethod(.Object, ...) > 19: eval(expr, envir, enclos) > 18: eval(call, callEnv) > 17: callNextMethod(.Object, ...) > 16: .local(.Object, ...) > 15: .nextMethod(.Object, assayData = assayData, phenoData = phenoData, > featureData = featureData, experimentData = experimentData, > annotation = annotation, protocolData = protocolData) > 14: eval(expr, envir, enclos) > 13: eval(call, callEnv) > 12: callNextMethod(.Object, assayData = assayData, phenoData = phenoData, > featureData = featureData, experimentData = experimentData, > annotation = annotation, protocolData = protocolData) > 11: .local(.Object, ...) > 10: .nextMethod(.Object, assayData = assayData, phenoData = phenoData, > featureData = featureData, experimentData = experimentData, > annotation = annotation, protocolData = protocolData) > 9: eval(expr, envir, enclos) > 8: eval(call, callEnv) > 7: callNextMethod(.Object, assayData = assayData, phenoData = phenoData, > featureData = featureData, experimentData = experimentData, > annotation = annotation, protocolData = protocolData) > 6: .local(.Object, ...) > 5: initialize(value, ...) > 4: initialize(value, ...) > 3: new("AffyBatch", cdfName = cdfname, annotation = cleancdfname(cdfname, > addcdf = FALSE)) > 2: just.rma(filenames = l$filenames, phenoData = l$phenoData, description = > l$description, > notes = notes, compress = compress, rm.mask = rm.mask, rm.outliers = > rm.outliers, > rm.extra = rm.extra, verbose = verbose, normalize = normalize, > background = background, bgversion = bgversion, destructive = > destructive, > cdfname = cdfname) > 1: justRMA() >> > > *> sessionInfo() > *R version 2.13.1 (2011-07-08) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=Spanish_Argentina.1252 LC_CTYPE=Spanish_Argentina.1252 > LC_MONETARY=Spanish_Argentina.1252 > [4] LC_NUMERIC=C LC_TIME=Spanish_Argentina.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] affy_1.30.0 Biobase_2.10.0 > > loaded via a namespace (and not attached): > [1] affyio_1.20.0 preprocessCore_1.14.0 tools_2.13.1 >> > > > > > Prof. Julio Di Rienzo > Estad?stica y Biometr?a > FCA- U.N. C?rdoba > IBS-RARG President > http://sites.google.com/site/juliodirienzo > "Biometry, the active pursuit of biological > knowledge by quantitative methods." > (R.A. Fisher, 1948) > > [[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 -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
ADD COMMENTlink written 7.0 years ago by Martin Morgan ♦♦ 22k
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