Bio::Affymetrix::CDF::Probe- an Affymetrix probe in a probeset in an CDF file
use Bio::Affymetrix::CDF;
# Parse the CDF file
my $cdf=new CDF();
$cdf->parse_from_file("foo.cdf");
# Find a probe. This is the first probe in the first probepair in Unit 1000
my $probe=$chp->probesets()->{1000}->[0]->[0];
# Find some fun facts about this probe
print join ",", ($probe->x(),$probe->y(),($probe->is_mismatch()?"Mismatch probe":"Perfect match probe");
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. Each probeset then contains an array reference of probepairs, each one which is an array reference of Bio::Affymetrix::CDF::Probe objects.
You can only get probe-level information if you have parsed the CDF object with probe-level parsing turned on.
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 [0] : none Example : my $probe=new Bio::Affymetrix::CDF::Probe(); Description: constructor for Bio::Affymetrix::CDF::Probe object. You probably do not want to make these objects yourself, however. Returntype : new Bio::Affmetrix::CDF object Exceptions : none Caller : general
To install Bio::Affymetrix::CEL, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Affymetrix::CEL
CPAN shell
perl -MCPAN -e shell install Bio::Affymetrix::CEL
For more information on module installation, please visit the detailed CPAN module installation guide.