[BioC] Affymetrix Gene array probe coordinates, mogene10stv1probe

[Leo Schalkwyk [guest]]

As far as I can see, there isn't a convenient source of mappings of the individual probes
of the Affymetrix Mouse Gene (and probably others) array onto the current genome build.  The package mogene10stv1probe is derived directly from the manufacturer's probe tab file which is based on old mm8 coordinates.  This fact is documented in the original file but not in the package.  

The coordinates could be lifted over, or better yet remapped.  Actually Ensembl maintains a nice mapping: http://www.ensembl.org/info/docs/microarray_probe_set_mapping.html  This can be accessed programatically through their perl API but not as far as I can figure out via biomaRt.

Since Ensembl has taken on the headache of maintaining a mapping, can anyone suggest a convenient way of making it available for analysis in R?  I can of course download the coordinates I need by hand, but I'm sure others have been held up by the same problem.

Leo

 -- output of sessionInfo(): 

> sessionInfo()
R version 2.14.0 (2011-10-31)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.ISO8859-1/en_US.ISO8859-1/en_US.ISO8859-1/C/en_US.ISO8859-1/en_US.ISO8859-1

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] mogene10stv1probe_2.9.0 AnnotationDbi_1.16.10   Biobase_2.14.0         
[4] BiocInstaller_1.2.1    

loaded via a namespace (and not attached):
[1] DBI_0.2-5      IRanges_1.12.5 RSQLite_0.11.1 tools_2.14.0  


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