[BioC] affylmGUI annotations

[James W. MacDonald]

Hi Ed,

On 8/23/2011 11:42 AM, 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?

The ST arrays are a bit of an edge case. The affy package was never 
intended for this chip design, and we don't really support it like we do 
the 3'-biased arrays.

By that I mean that we do supply cdf packages, and there is an 
annotation package that you can use, but the annotation package isn't 
named according to the rules used by the affy package, so affylmGUI 
isn't finding it.

The package you want is called mogene10sttranscriptcluster.db (according 
to the naming rules for the affy package, it will likely be looking for 
mogene10v1st.db). I know nothing of the affylmGUI package, having never 
used it, so I don't know if there is an easy way to tell it that the 
annotation package has an unexpected name.

So your recourse at this point is to play around with affylmGUI, and see 
if you can tell it the correct annotation package to use, or wait for 
Keith Satterley to respond. As the maintainer, he is most likely to know 
what to do.

Other alternatives may be less palatable, as you evidently like a GUI 
interface. However, the oligo and xps packages are directly designed to 
work with these chips so won't have this problem.

Hypothetically you could also download the source package for 
mogene10sttranscriptcluster.db, rename things to coincide with what 
affylmGUI is expecting, build and install. But if you are going to do 
that, you might as well save time and energy by just switching to 
command-line based packages that are more amenable to working with this 
chip.

Best,

Jim



>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor

-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues