[BioC] Problems annotating a gene list

James W. MacDonald jmacdon at med.umich.edu
Fri Feb 24 23:19:52 CET 2006

Hi Quentin,

You might look at limma2annaffy() in the affycoretools package. It will 
take your design matrix, contrast matrix, exprSet, and MArrayLM objects 
and output HTML and/or text tables with all the probesets annotated.

This package is in the devel repository, so you will not be able to get 
it using e.g., biocLite() unless you are running R-2.3.0dev. However, it 
doesn't require the devel version of R, so you can download by hand and 
install using either the dropdown menu (if you are using win32) or R CMD 
INSTALL if you are on a Unix variant.



Sean Davis wrote:
> On 2/24/06 12:58 PM, "Quentin Anstee" <q.anstee at imperial.ac.uk> wrote:
>>Hi Sean,
>>Thanks for coming back to me on this one.
>>I have had a look at 'fit2$genes', all it contains are the affy probe IDs as
>>you predicted. Could you describe how to make the annotations and attach
>>them to the MArrayLM file or let me know where this process is described? I
>>have had a look in the limma help files and vignette but have not been able
>>to find a walk through of this procedure.
> It will suffice to make a data.frame in the same order and containing the
> same number of genes at fit2$genes.  If your new data.frame is called
> gene.data, you just say fit2$genes <- gene.data.
> You might want to look at the annaffy package and vignette for some ideas
> about how to ge the information you want from the annotation package.
> Sean
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James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109

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