NAME

Bio::Affymetrix::CDF::Probeset- an Affymetrix probeset in an CDF file

SYNOPSIS

use Bio::Affymetrix::CDF;

# Parse the CDF file

my $cdf=new CDF();

$cdf->parse_from_file("foo.cdf");

# Print out all of the probeset names on this chip type

my $probeset=$chp->probesets()->[0];

FINISH ME HERE

DESCRIPTION

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 list of Bio::Affmetrix::CDF::Probeset objects. This allows you look at the details of the probeset.

HINTS

You can only get probe-level information if you have parsed the CDF object with probe-level parsing turned on.

COPYRIGHT

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.

AUTHORS

Nick James (nick at arabidopsis.info)

David J Craigon (david at arabidopsis.info)

Nottingham Arabidopsis Stock Centre (http://arabidopsis.info), University of Nottingham.

METHODS

new

  Arg [0]    : 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 object
  Exceptions : none
  Caller     : general

unit_name Arg [1] : string $unit_name (optional) Example : my $unit_name=$ps->unit_name() Description: Always NONE for expression arrays Returntype : string Exceptions : none Caller : general

is_sense Arg [1] : boolean $sense (optional) Example : if ($ps->is_sense()) { .... } Description: Returns true when this is a sense (rather than anti-sense) probeset Returntype : boolean Exceptions : none Caller : general

original_num_probepairs Arg [0] : none Example : my $probepairs=$ps->original_num_probepairs() Description: Get the number of probepairs in this probeset Returntype : integer Exceptions : none Caller : general

original_num_probes Arg [0] : none Example : my $probepairs=$ps->original_num_probes() Description: Get the number of probes in this probeset Returntype : integer Exceptions : none Caller : general

unit_number Arg [0] : none Example : my $probepairs=$ps->unit_number() Description: Get the unit number of this probeset (a unique number assigned to each probe in the CDF file but otherwise meaningless) Returntype : integer Exceptions : none Caller : general

mutation_type Arg [0] : integer Example : none Description: Get/set mutation_type. If this is a genotyping probe set, 0=substitution, 1=insertion, 2=deletion Returntype : integer Exceptions : none Caller : general

name Arg [1] : string Example : my $name=$ps->name() Description: Get/set name of probeset Returntype : string Exceptions : none Caller : general

probes Arg [1] : arrayref $probelist Example : my @probes=$ps->probes() Description: Get/set list of probes making up this array. Only available if with probes mode is used. Returntype : reference to array of Bio::Affymetrix::CDF::Probe objects Exceptions : none Caller : general

CDF Arg [1] : Bio::Affymetrix::CDF object $probelist Example : my $cdf=$ps->probes() Description: Get/set CDF object this probeset belongs to. Returntype : Bio::Affymetrix::CDF object Exceptions : none Caller : general

CPAN RT