[BioC] Missing GeneSymbol and Name information in TopTable

[Marc Carlson]

Hi Kai,

What happens if you just type:

library("hgu133plus2.db")

To load the library before you run whatever it is that you are running?

Also, history() should display the code from your session.  Which you
could then post so that the rest of us would know what you were trying
to do.


  Marc


 
Kai Treuner wrote:
> Hi Marc,
> I went ahead and downloaded the "hgu133plus2.db" package again:
>
> package 'hgu133plus2.db' successfully unpacked and MD5 sums checked
> updating HTML package descriptions
>
> However, here is still the same session info:
>
> 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         
> 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
>
>
> Which command would show the code?
> Kai
>
>
>
>
> -----Original Message-----
> From: Marc Carlson [mailto:mcarlson at fhcrc.org] 
> Sent: Friday, August 21, 2009 9:33 AM
> To: Kai Treuner
> Cc: Sean Davis; bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] Missing GeneSymbol and Name information in TopTable
>
> 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
>>
>>
>>
>>
>>
>> 	[[alternative HTML version deleted]]
>>
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