[Bioperl-l] Pasing Affymatrix Microarray output

Steve Chervitz sac at bioperl.org
Wed Apr 8 01:59:49 EDT 2009

Check out our Affymetrix Power Tools (APT) package:


We distribute binaries for Linux and Mac OSX, as well as source code
so you can compile it yourself if you want. Note however that this is
written in C++, not Perl.  We don't provide SWIG or XS interfaces for
direct access via Perl, though this would definitely be doable, if
anyone is interested.

Probably the easiest approach from Perl would be to simply call the
appropriate APT executable through the shell as in:

    system("/path/to/apt --args ...");

The Perl code can parse the output files and take it from there.


On Tue, Apr 7, 2009 at 7:10 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> On Tue, Apr 7, 2009 at 9:39 PM, Wen-Zhi WANG <wenzhiwang1983 at yahoo.com.cn>wrote:
>> Dear all,
>> Recently, I focus on population genomics data outputed by affymatrix
>> microarray system. However, softwares which designed by affy. inc only run
>> in Windows 386 platform. Is there any application can used in Linux?
>> Bio::Affymatrix was not strong enough to get the detailed informaton.
> You may want to look at a non-bioperl solution such as Bioconductor (
> http://bioconductor.org).
> Sean
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