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

Question:

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.

mblanche@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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Received on Wed Jul 26 10:26:04 2006

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