[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.
HTH,
Jim
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
734-647-5623
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