[BioC] Drosophila Genome 2.0 annaffy annotation

James W. MacDonald jmacdon at med.umich.edu
Wed Jul 26 20:33:30 CEST 2006


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 can¹t 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 ³drosophila2²
> 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
> 
> 
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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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