[BioC] ReadAffy() Problem

[smohapat at vbi.vt.edu]

Hello Alex:

Is it possible that the PC and the server run different versions of affy
package? looking at sessionInfo() output might help.

Best wishes,

Saroj

On Sun, July 1, 2007 1:07 pm, ssls sddd wrote:
> 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
>
>
> [[alternative HTML version deleted]]
>
>
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