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"James W. MacDonald" <jmacdon at="" med.umich.edu=""> writes: > Well, it is supposed to. Unfortunately, there is a small bug there that > is keeping things from working correctly (fixed in the devel > repository). Any volunteers for fixing this in the release? > Anyway, you can do one of two things. > > library(reposTools) > Symbol <- aafSymbol(geneIDs, "drosophila2") I do not recommend this approach. reposTools is deprecated. Try the biocLite approach: > source("http://www.bioconductor.org/biocLite.R") > biocLite("drosophila2") > Symbol <- aafSymbol(geneIDs, "drosophila2") Best, + seth

Hi Marco, Marco Blanchette wrote: > Dear all, > > I am currently analyzing a set of arrays hybe on the lattest affy Drosophila > 2.0 GeneChip. I am trying to run simple annaffy analysis but can?t find what > is the name of the annotation file I need to use. > > Here is the output of the AffyBatch object I am using: > >>expData > > AffyBatch object > size of arrays=732x732 features (16749 kb) > cdf=Drosophila_2 (18952 affyids) > number of samples=4 > number of genes=18952 > annotation=drosophila2 > > So when I try to use and annaffy procedure I get: > > >>Symbol = aafSymbol(geneIDs, "drosophila2") > > [1] "You are missing drosophila2 looking to see if it is available." > Error in chkPkgs(chip) : couldn't find function "userQuery" > > In the annaffy documentation, it is specified that the constructor will try > to load the annotation. Well, it is supposed to. Unfortunately, there is a small bug there that is keeping things from working correctly (fixed in the devel repository). Anyway, you can do one of two things. library(reposTools) Symbol <- aafSymbol(geneIDs, "drosophila2") -or- source("http://www.bioconductor.org/biocLite.R") biocLite("drosophila2") Symbol <- aafSymbol(geneIDs, "drosophila2") Best, Jim > > Questions: > 1) Am I using the right annotation file ie ?drosophila2? > 2) Do I need to install the drosophila2 annotation before trying to use it. > 3) If so, what is the procedure > > Suggestion: the annaffy vignette could be a bit more specific about the > annotation file. > > Many thanks > > ______________________________ > Marco Blanchette, Ph.D. > > mblanche at uclink.berkeley.edu > > Donald C. Rio's lab > Department of Molecular and Cell Biology > 16 Barker Hall > University of California > Berkeley, CA 94720-3204 > > Tel: (510) 642-1084 > Cell: (510) 847-0996 > Fax: (510) 642-6062 > > > -------------------------------------------------------------------- ---- > > _______________________________________________ > 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.