[BioC] affymetrix_expression data outfile_annotation

James W. MacDonald jmacdon at med.umich.edu
Fri Jan 25 16:07:38 CET 2008

Hi Sebastien,

Sébastien Tourlet wrote:
> hello 
> I start some studies on affymetrix chips. I have not found how to put gene names into the gene expression output file in order to do a link between affyid and gene names.
> Could you help me on it?

You want an annotation package and mget().

Say your chip is the hgu133plus2, and you have a vector of probe ids 
called 'prbs'.

library(hgu133plus2.db) #use biocLite() to get it if necessary.
symb <- mget(prbs, hgu133plus2SYMBOL)

will give you a list of gene symbols for each probe id. You can see all 
the mappings available by typing hgu133plus2().

Alternatively, you can use probes2table() in affycoretools to output 
either text or HTML tables.



> Thanks in advance for your reply
> Best regards
> Sébastien
> 	[[alternative HTML version deleted]]
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James W. MacDonald, M.S.
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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