[Bioc-devel] Creating platformDesign for Affy Tiling from AtEnsembl

[sneumann]

Hi,

We have hybridizations done with 
the Affymetrix Arabidopsis Tiling chip.  

I have created a pd.at35b.mr.v04 package 
from the Affy BPMAP file using makePDpackage()
from makePlatformDesign() and this works fine.

However, The BPMAP is based on Genome Release TAIR5.
In http://atensembl.arabidopsis.info/ the probe sequences 
of the tiling chip have been blasted against the TAIR7 release,
and are available e.g. as GFF file 
or via a (local) ensemble installation.

Is there a (convenient) way to create a PDpackage
from these GFF data ? Any Code I could adapt ?

Yours,
Steffen








-- 
IPB Halle                    AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann          http://www.IPB-Halle.DE
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