[BioC] Wheat annotation

[James W. MacDonald]

Hi Sam,

On 6/12/2012 8:58 PM, Sam McInturf [guest] wrote:
> Hello,
>    I am working on a set of Affymetrix wheat array, with some very ancient annotations included.  I have been looking, and many sequenced organisms have a xxx.db annotation package that is used in conjunction with annotationDBi.  I have found the wheatcdf, which seems to describe the environment (probe mapping), but this does not seem to be the same information as the xxx.db has.  Is there such a package, or is wheat without such annotations?

There is no such package. These packages depend on some fairly extensive 
infrastructure (they need an organism-level .db package, as well as an 
intermediate 'db0' package that Marc Carlson makes). Which packages have 
been supported is based on the cost/benefit where benefit is defined 
loosely as the number of end users who are likely to use the package. 
Unfortunately anopheles and yeast are the only plants to have jumped 
that hurdle so far.

I checked the biomaRt package as well, and I don't see any support for 
Triticum there either. You could always just do something bootleg like 
downloading the annotations from Affy

http://www.affymetrix.com/analysis/downloads/na32/ivt/wheat.na32.annot.csv.zip

and parsing by hand.

Best,

Jim

>
> Thanks!
> Sam
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099