[BioC] package for human ST gene arrays?

[Mark Robinson]

You can analyze the Gene 1.0 ST chips within the 'aroma.affymetrix'  
package also:

http://groups.google.com/group/aroma-affymetrix/web/hugene-1-0-st

No restrictions within aroma.affymetrix for probes shared b/w  
probesets. There is a bit of work to do to set this up (CDFs, etc),  
but let me know if you want to go this route.

Cheers,
Mark


On 27/10/2007, at 12:05 AM, James W. MacDonald wrote:

> Hi Yongde Bao,
>
> There is a new package xps in the Devel repository that is intended  
> for
> the analysis of the gene arrays. To use this package you will need
> R-devel, as well as installing ROOT. There are clear instructions for
> building the package on *NIX as well as MacOSX, but if you want to run
> on Windows you will have to figure things out for yourself.
>
> In addition, someone has already posted links to cdf packages for this
> chip that will allow you to use the affy package. Note however that  
> some
> of the probes on this chip are shared between probesets, and that was
> not true in the past, so for a certain percentage of probesets you  
> will
> be missing probes (once a probe is allocated to a probeset, it will  
> not
> be available for any other probesets).
>
> Best,
>
> Jim
>
>
>
>
> Yongde Bao wrote:
>> Hi all,
>>
>> I wonder if there is any package in Bioconductor that deals with  
>> the analysis
>> of the Affy Human ST gene arrays. If so can someone point out  
>> where to get it?
>>
>> Best regards,
>>
>> Yongde Bao
>> University of Virginia
>>
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>
> -- 
> James W. MacDonald, M.S.
> Biostatistician
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623
>
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