[BioC] AffyBatch: Replacing probe set IDs with Genebank

[Aedin]

Hi Jeppe
To get from affyIDs' to genbank accession numbers:

If there is a metadata package for your Affymetrix chip (you can get the
metadata from the BioC website or using install.packages2())

Eg for package hgu133a
library(hgu133a)

Then use:

hgu133aGENENAME()
hgu133aACCNUM()


Alternatively use annaffy() which is an excellent package

library(annaffy)

Then use either:

aafGenBank(probesidlist, "hgu133a")
aafSymbol(probesidlist, "hgu133a")

If you've a custom chip, you may need to use AnnBuilder create the
metadata yourself.
Hope this helps
Aedin






Date: Thu, 3 Mar 2005 11:57:16 +0100
From: "JSPC (Jeppe Skytte Spicker)" <jspc at novonordisk.com>
Subject: [BioC] AffyBatch: Replacing probe set IDs with Genebank
	Accesion	numbers?
To: <bioconductor at stat.math.ethz.ch>
Message-ID:
	<CE4C1B6620E59840BB07F6F12256AEDF026B618A at exdkba021.novo.dk>
Content-Type: text/plain;	charset="us-ascii"

Hi All

How do I get from the probe set IDs in the AffyBatch at exprs to e.g.
Genebank acc. numbers?

I would like to be able to make the replacement using the .GIN file
because I am also looking at custom affy chips.

Thank you in advance.

Best regards Jeppe