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

sneumann sneumann at ipb-halle.de
Wed Oct 24 11:27:44 CEST 2007


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 ?


IPB Halle                    AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann          http://www.IPB-Halle.DE
Weinberg 3                   http://msbi.bic-gh.de
06120 Halle                  Tel. +49 (0) 345 5582 - 1470
                                  +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409

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