[R] Can't make affylmGUI work

[Martin Morgan]

Feifei -- 

Ask on the Bioconductor mailing list http://bioconductor.org. Update
your Bioc packages following instructions on the 'install - how to'
page linked from the main bioconductor page -- your affy is out of
date.

Best, Martin

Feifei <clarezoe at gmail.com> writes:

> Hi,
>
> Can anyone help me of the affylmGUI package, I can't get it work and
> searched for google but can't find any proper solutions.
>
> I get the error information each time when I load my cells files, which
> are shown in the following links.
> -------------
> http://clarezoe.googlepages.com/1.png
> http://clarezoe.googlepages.com/2.png
> http://clarezoe.googlepages.com/3.png
> -------------
>
> Errors also show in the terminal as below,
> -------------
>  > Error: no function to return from, jumping to top level
>   In addition: Warning messages:
>   1: read.phenoData is deprecated, use read.AnnotatedDataFrame instead 
>   2: The phenoData class is deprecated, use AnnotatedDataFrame (with
> ExpressionSet) instead 
>   Error in exprs(RawAffyData) : 
>   no function to return from, jumping to top level
> --------------
>
> I'm running R version 2.6.1 under Linux Ubuntu 7.10
>
> --------------
>
> My sessionInfo is shown below,
>
> --------------
>  > sessionInfo()
>  R version 2.6.1 (2007-11-26) 
>  i486-pc-linux-gnu 
>
>  locale:
>
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
>  attached base packages:
>  [1] tools     tcltk     stats     graphics  grDevices utils
> datasets 
>  [8] methods   base     
>
>  other attached packages:
>  [1] affylmGUI_1.12.0 affy_1.12.2      affyio_1.6.1     Biobase_1.16.1  
>  [5] limma_2.12.0    
>
>  loaded via a namespace (and not attached):
>  [1] rcompgen_0.1-17
> ----------------
>
> Can anyone help me with that? I really need it to work ASAP.
>
> Thanks a lot!
>
> Sincerely 
> Feifei
>
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