[BioC] how do you make a decoding dataframe affy2locusDF

[James W. MacDonald]

Hi Caroline,

Caroline Reiff wrote:
> Hi, I am trying to learn how to use the GoHyperGALL function and 
> while it works fine with the arabidopsis example data I am not 
> managing to get it to work for chips other than arabidopsis. I am 
> stuck with the following- how do I obtain AffyID-toGeneID mappings 
> for chips other than arabidopsis, i.e how do you make a decoding 
> dataframe affy2locusDF (see below from 
> http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/R_BioCondManual.html#biocon_limmaaffy

AFAIK, GOHyperGAll isn't part of BioC. Have you asked Thomas Girke how 
to do this?

Best,

Jim


> 
> "Obtain AffyID-to-GeneID mappings when working with AffyIDs
> AffyID2GeneID(map = 
> "ftp://ftp.arabidopsis.org/home/tair/Microarrays/Affymetrix/affy_ATH1_array_elements-2006-07-14.txt") 
> # When working with AffyIDs, this function creates a AffyID-to-GeneID 
> mapping data frame using by default the TAIR mappings for the 
> Arabidopsis ATH1 chip. To use the function for the mappings of other 
> chips, one needs to create the corresponding decoding data frame 
> 'affy2locusDF'."
> Thanks Caroline
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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