[BioC] how build annotation package

John Zhang jzhang at jimmy.harvard.edu
Wed May 5 20:34:26 CEST 2004

>Just want to know if anybody has written a step by step instruction to build a 
affymetrix annotation package. We have some moe430_2 chips (as well as the 
library files) from affymetrix, but I can not find its annotation package from 
bioconductor meta data section. Seems the instruction of How to use Annbuilder 
only apply after you have data with specific format (such as two columns). But 
now I only have the chip library file.  

I do not know what you have, but I got all the two-column mappings between 
AffyMetrix probe ids and GenBank, UniGene, or LocusLink ids from AffyMetrix 
(http://www.affymetrix.com/support). For each chip, AffyMetrix has an annotation 
file (e. g. Mouse430_2 Annotations, CSV (10 MB, 4/29/04)) that contains the 
mappings. You just need to extract the mappings you want (e. g. two column 
mappings between probe ids and GenBank accession numbers), make a tab (or ;, 
...) separated file, and then go from there.  

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Jianhua Zhang
Department of Biostatistics
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084

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