[Bioperl-l] looking for modules to retrieve signals and genomic positton for each probe in the probe set of Affymetrix Array

Sean Davis sdavis2 at mail.nih.gov
Wed Oct 19 11:02:42 EDT 2005

On 10/19/05 10:11 AM, "szhan at uoguelph.ca" <szhan at uoguelph.ca> wrote:

> Hello, Bioperl Users,
> I am analyzing gene expression raw data (.cel and .cdf file) of Affymetrix
> genome gene expression array.
> Do you know which bioperl module (or another way) can retrieve the signals and
> genomic position for each probe pair in the probe set of th Affymetrix array?
> I
> read the perldoc for Bio::Affymetrix module. It seems that it can only
> retrieve
> the signals for the probe set, not for each probe and its genomic postion. I
> also have a problem to install this module (Bio-Affymetrix-0.5.tar) on PC
> running Windows XP, Perl 5.8 and Bioperl 1.4.
> Any information will be high appreciate!
> Joshua

Your best bet for working with affymetrix arrays is to use R
(http://www.r-project.org) and Bioconductor (http://www.bioconductor.org).
These packages provide MANY, MANY functions for dealing with affymetrix
arrays from normalization to analysis to annotation.

Mapping probes to genomic position is frought with difficulty, as 20-mers
will typically align many places in the genome at some threshold.  That
said, I think that Ensembl does this mapping, if you are interested.  You
can use their public mysql server to access these data, if I recall.


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