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)

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