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.htm l#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

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.h tml#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_ATH 1_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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- 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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.