[BioC] package for human ST gene arrays?

[Kasper Daniel Hansen]

On Oct 26, 2007, at 9:06 AM, Yongde Bao wrote:

> 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?

aroma.affymetrix runs in windows (the main developer is using  
windows), and if you want a look at the output why don't you follow  
the link Mark gave you and read some of the pages.

It also allows analysis of very large datasets on a laptop (given  
around 1-2GB ram)

Kasper

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