[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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