Bio::Affymetrix::CDF::Probeset- an Affymetrix probeset in an CDF file
# Parse the CDF file
my $cdf=new Bio::Affymetrix::CDF();
# Print out the probeset name of Unit 1001
The Affymetrix microarray system produces files in a variety of formats. If this means nothing to you, these modules are probably not for you :). After these modules have parsed a CDF file, the resulting Bio::Affymetrix::CDF file contains a hash of Bio::Affmetrix::CDF::Probeset objects, keyed on the unit number. This allows you look at the details of the probeset.
If you have parsed a CDF file with probe-level parsing turned on, you can examine the individual probes using the probes method. By altering the contents of this array, you can redesign the chip! NASC use this in our cross-species work (http://affymetrix.arabidopsis.info/xspecies).
You can only get probe-level information if you have parsed the CDF object with probe-level parsing turned on.
The probe level parsing interface is a bit inelegant at the moment. This might change in future versions.
Copyright (C) 2005 by Nick James, David J Craigon, NASC (arabidopsis.info), The University of Nottingham
This module is free software. You can copy or redistribute it under the same terms as Perl itself.
Affymetrix is a registered trademark of Affymetrix Inc., Santa Clara, California, USA.
Nick James (nick at arabidopsis.info)
David J Craigon (david at arabidopsis.info)
Nottingham Arabidopsis Stock Centre (http://arabidopsis.info), University of Nottingham.
Arg  : none Example : my $cdf=new Bio::Affymetrix::CDF::Probeset(); Description: constructor for Bio::Affymetrix::CDF::Probeset object. You probably do not want to make these objects yourself yet, however. Returntype : new Bio::Affmetrix::CDF::Probeset object Exceptions : none Caller : general
Returns an reference to an array of "probe pairs". Each "probe pair" is an array reference containing two Bio::Affymetrix::CDF::Probe objects. The design of the CDF file implies that one point chips with 3 mismatch probes and one perfect match probe were mooted, but we are unsure whether any of these were ever released to the public. Nevertheless, these modules are ready! Returntype : reference to array of arrayrefs of Bio::Affymetrix::CDF::Probe objects Exceptions : none Caller : general