[BioC] package for human ST gene arrays?

[James W. MacDonald]

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