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@gmail.com] 
Sent: Thursday, August 20, 2009 5:55 PM
To: Kai Treuner
Cc: bioconductor@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@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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