[BioC] how do you make a decoding dataframe affy2locusDF

Caroline Reiff C.Reiff at rri.sari.ac.uk
Fri Jan 26 18:49:04 CET 2007


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

"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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