[BioC] Missing GeneSymbol and Name information in TopTable

[Marc Carlson]

Hi Kai,

I still don't see your code, but just from your sessionInfo(), it does
not appear that you really have the "hgu133plus2.db" package loaded. 
And as you noted in your previous post, it appears that this is what the
error message is asking about.


  Marc




Kai Treuner wrote:
> Hi Sean,
>
> Here is the session info. Am I missing a specific package to get the
> Gene Symbols and names?
>
> Thanks, Kai
>
>  
>
> R version 2.9.1 (2009-06-26) 
>
> i386-pc-mingw32 
>
>  
>
> locale:
>
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
>  
>
> attached base packages:
>
> [1] tcltk     stats     graphics  grDevices utils     datasets  methods
>
>
> [8] base     
>
>  
>
> other attached packages:
>
> [1] tkrplot_0.0-18       hgu133plus2cdf_2.4.0 affylmGUI_1.18.0    
>
> [4] affyio_1.12.0        affy_1.22.1          Biobase_2.4.1       
>
> [7] limma_2.18.2        
>
>  
>
> loaded via a namespace (and not attached):
>
> [1] preprocessCore_1.6.0 tools_2.9.1
>
>  
>
> ________________________________
>
> From: Sean Davis [mailto:seandavi at gmail.com] 
> Sent: Thursday, August 20, 2009 5:55 PM
> To: Kai Treuner
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] Missing GeneSymbol and Name information in TopTable
>
>
>
>
>
> On Thu, Aug 20, 2009 at 8:15 PM, Kai Treuner
> <ktreuner at braincellsinc.com> wrote:
>
> Hi,
> I am trying to get the gene symbols and names of genes included in the
> TopTable. I am using affylmGUI package under R 2.9.1 on windows XP. Even
> after downloading the hgu133plus2.db annotation file as well as the
> annotate, annaffy and other packages it doesn't work.
>
> These are the error messages:
> Error in text(A[topGenes],M[topGenes], labels= substr(genelist[topGenes,
> : object 'topGenes' not found
>
> Warning messages:
> 1: In getDependencies(pkgs, dependencies, available, lib) :
>  package 'hgu133plus2' is not available
> 2: In getDependencies(pkgs, dependencies, available, lib) :
>  package 'hgu133plus2' is not available
>
>
> Hi, Kai.  
>
> You'll want to give the code that you are using for your analysis as
> well as the output of sessionInfo().
>
> Sean
>
>
>
>
>
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