Jim,

Thanks a lot! I'll try them. 

-James

--- On Fri, 7/9/10, James W. MacDonald <jmacdon@med.umich.edu> wrote:

From: James W. MacDonald <jmacdon@med.umich.edu>
Subject: Re: [BioC] how to do probe set mapping between U133A and Gene 1.0 ST array
To: "James Anderson" <janderson_net@yahoo.com>
Cc: "bioconductor" <bioconductor@stat.math.ethz.ch>
Date: Friday, July 9, 2010, 5:44 PM

Hi James,

On 7/8/2010 12:23 PM, James Anderson wrote:
> Hi,
> 
> I am new to Gene 1.0 ST array, could anyone give some suggestion on how to map the probe sets from U133A to Gene 1.0 ST array?

I think this is easier said than done, particularly since the 133a probes are all clustered on the 3' end of the transcript, whereas the gene array probes span the transcript. Plus, the 133a was superceded by the 133plus2 years ago, so most affy support is directed towards the 133plus2.

So I guess it depends on what you mean exactly by 'map'. Some ideas, from most simple to most difficult (and likely missing other solutions):

1.) Simply map gene symbol (Entrez Gene ID, whatever) between the two platforms using the annotation.db packages.

2.) Use the 'Best match' (or complex match, good match, etc) tables that affy supplies (for the 133plus2 --> Gene ST, you need to do the 133a --> u133plus2 separately). These can be found on the affy support site:

Start here:

http://www.affymetrix.com/support/index.affx#1_2

then under Affymetrix Microarray Solutions, click Support Documents. Then select the Gene 1.0 ST chip in the list box and hit Go. The inter-chip match files will be on the resulting page.

3.) Just do it yourself using the Biostrings, BSgenome and individual probe packages. This will take some work on your part, but for the right individual might be interesting and/or fun.

This will be more critical if you mean something more than 'these two probesets interrogate the same gene transcript' when you say 'map'.

Best,

Jim




> 
> Thanks,
> 
> -James
> 
> 
> 
> 
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> 
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-- James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
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