[BioC] adding annotation to exprSet

James W. MacDonald jmacdon at med.umich.edu
Tue Aug 9 22:39:25 CEST 2005

Andreas Zankl wrote:
> In the limma Vignette chapter 21.2, the ApoAI dataset contains gene 
> names. How did they get in there? This is exactly what I am trying to 
> achieve.

You could use the genelist argument of topTable. I wouldn't recommend 
using the actual gene name, because they can be quite long - instead I 
would use the gene symbol. However the choice is up to you.

genenames <- sapply(mget(ls(hgu133plus2GENENAME), hgu133plus2GENENAME, 
ifnotfound = NA), function(x) x[1])

topTable(fit, genelist = genenames)

For the symbol, you do the above but substitute hgu133plus2SYMBOL.



> Thanks
> Andreas
>>Can somebody tell me how to add annotation to an affy exprSet? I 
>>would like to see the gene name in the limma topTable output. I 
>>looked at the annotate documentation and tried all kind of 
>>manipulations on the hgu133plus2 datafile, but I can't get it to 
>>Hope you can help.
>>Many thanks
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James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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