[R] Drosophila Genome 2.0 annaffy annotation

From: Marco Blanchette <mblanche_at_berkeley.edu>
Date: Wed 26 Jul 2006 - 09:45:22 EST

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 canıt 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

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 documentation it is specified that the constructor will try to load the annotation.


1)Am I using the right annotation file ie ³drosophila2²
2) Do I need to install it before trying to use it.
3) If so, what is the procedure

Many thanks

Marco Blanchette, Ph.D.


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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Received on Wed Jul 26 10:26:04 2006

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