[BioC] justRMA {affy} error

[Martin Morgan]

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
> 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]]
>
>
>
>
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