[BioC] package for human ST gene arrays?

[Henrik Bengtsson]

On 10/26/07, Yongde  Bao <yb8d at virginia.edu> 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?

Yes, your questions are answers on the front page:

  http://groups.google.com/group/aroma-affymetrix/

Cheers

/Henrik

>
> 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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> >>> 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
> >>
> >> _______________________________________________
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> >> gmane.science.biology.informatics.conductor
> >
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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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