Hi Sean,

For the second option, is there a specific package that you had in mind? Perhaps the GenomicFeatures package, which can download UCSC tables.


Thanks,
Pete
________________________________
From: seandavi@gmail.com [seandavi@gmail.com] on behalf of Sean Davis [sdavis2@mail.nih.gov]
Sent: Wednesday, July 21, 2010 7:27 AM
To: Bazeley, Peter
Cc: bioc-devel@stat.math.ethz.ch
Subject: Re: [Bioc-devel] mapping probes/probesets between platforms



On Tue, Jul 20, 2010 at 10:50 PM, Bazeley, Peter <Peter.Bazeley@rockets.utoledo.edu<mailto:Peter.Bazeley@rockets.utoledo.edu>> wrote:
Dear List,

What packages/approaches are recommended for mapping probes/probesets between 2 microarray platforms? Currently, I am using GenBank Accession IDs and UniGene IDs if these are not present.


Hi, Peter.

There is not a standard.  However, there are two broad approaches for gene id mapping.  The first is to map between common transcript ids (enst, refseq, ucsc known gene, etc) and the second is to map between common gene ids (unigene, ensg, entrez gene id, hgnc gene symbol, etc.).  Using the platform-specific annotation packages, both of these approaches are quite easy.  As an aside, using genbank accessions will not likely be fruitful without mapping to gene first.

Another approach entirely is to realign the probe sequences to a transcript library such as refseq and use those mappings as the basis for translation between probes/probesets.

Sean

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