Dear List,

I have a problem with using ReadAffy() on a server. I don't have such
problem when running on a stand-alone PC machine. Please help.
Thanks!

Sincerely,

Alex





The code I ran:

library(affy)
mydata <- ReadAffy()

The error message is attached:

> library(affy)
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: reposTools

Attaching package: 'reposTools'


        The following object(s) are masked from package:Biobase :

         note,
         userQuery

> mydata <- ReadAffy()
Error in validObject(.Object) : invalid class "AffyBatch" object:
sampleNames different from names of phenoData rows
In addition: Warning messages:
1: read.phenoData is deprecated, use read.AnnotatedDataFrame instead
2: The phenoData class is deprecated, use AnnotatedDataFrame (with
ExpressionSet) instead
3: The exprSet class is deprecated, use ExpressionSet instead
4: The exprSet class is deprecated, use ExpressionSet instead
5: The exprSet class is deprecated, use ExpressionSet instead
6: The exprSet class is deprecated, use ExpressionSet instead
7: The exprSet class is deprecated, use ExpressionSet instead
8: The exprSet class is deprecated, use ExpressionSet instead

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