[BioC] package for human ST gene arrays?

[Yongde Bao]

Thanks, Jim and Mark, for the prompt response.

Mark, about the aroma.affymetrix package, does it run readily in Windows? And, 
if possible, can you show me a bit of the taste of its output?

Best, Yongde

On Sat, 27 Oct 2007 01:32:14 +1000
  Mark Robinson <mrobinson at wehi.EDU.AU> wrote:
> 
> 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
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at stat.math.ethz.ch
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives: http://news.gmane.org/ 
>>> gmane.science.biology.informatics.conductor
>>
>> -- 
>> 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
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: http://news.gmane.org/ 
>> gmane.science.biology.informatics.conductor
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: 
>http://news.gmane.org/gmane.science.biology.informatics.conductor

Yongde Bao, Ph.D.
Department of Microbilogy
Biomolecular Research Facility
University of Virginia
Voice Mail:434-982-2551
FAX:        434-982-2514