[BioC] affylmGUI annotations

Richard Friedman friedman at cancercenter.columbia.edu
Fri Aug 26 04:08:55 CEST 2011


 	I know what I am about to suggest soundds awkward but you can 
donwload the annotation from the affy web site, sort your outout by 
accesion #s and paste in the annotation aligned by accession number and
then resort by p-value.

With hopes that the above helps,

On Tue, 23 Aug 2011, Ed Siefker wrote:

> I am trying to analyze data from Affymetrix Mouse Gene 1.0 ST arrays.
> I am using R 2.13.0 with affylmGUI and all its dependencies freshly
> installed.  I have analyzed my data exactly as described in the
> Estrogen Worked Example from the documentation.
> I get no annotations on my toptable, just probeset ids.  I don't see
> any error messages about being unable to find or download annotations,
> or any indication that it has tried to annotate the data at all.
> Reading the documentation, the only other reference to annotation that
> I can find points me to http://www.bioconductor.org/data/metaData.html
> which does not exist.  How do I proceed from here?
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Richard A. Friedman, PhD
Associate Research Scientist
Herbert Irving Comprehensive Cancer Center
Biomedical Informatics Shared Resource
Department of Biomedical Informatics
Box 95, Room 130BB or P&S 1-420C
Columbia University Medical Center
630 W. 168th St.
New York, NY 10032
(212)305-6901 (5-6901) (voice)
friedman at cancercenter.columbia.edu

"The last 250 pages of the last Harry Potter
book took place in one day because alot
happened in that day. All of Ulysses takes
place in one day and nothing happened in that day."
-Rose Friedman, age 11

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