Probe documentation.

#### Bio::Affymetrix::CDF

### Probe

Summary | Package variables | Synopsis | Description | General documentation | Methods

Summary

    Bio::Affymetrix::CDF::Probe- an Affymetrix probe in a probeset in an CDF file

Package variables | top

No package variables defined.

Included modules | top

Carp
strict
warnings

Synopsis | top

    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");

Description | top

    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.

Methods | top

index | Description | Code
is_mismatch | Description | Code
mismatch_position | Description | Code
new | Description | Code
original_probe_number | No description | Code
original_probepair_number | Description | Code
original_probeset | Description | Code
probe_mismatch_base | Description | Code
probe_target_base | No description | Code
x | Description | Code
y | Description | Code

## Methods description

index | code | top | prev | next

        Arg [1]    :  integer $index (optional)
        Example    :  my $i=$probe->index();
     Description: 	Get/set the index of this probe. Allegedly this number
        was used in the CEL file at some point, but is probably useless now.
        Returntype : integer
        Exceptions : none
        Caller     : general

is_mismatch | code | top | prev | next

        Arg [0]    : none
        Example    : if ($probe->is_mismatch()) {
    print "Everybody loves mismatch probes!";
    }
      Description: 	Utility function that returns whether this probe is a
        mismatch probe or not.
        Returntype : bool
        Exceptions : none
        Caller     : general

mismatch_position | code | top | prev | next

        Arg [1]    :  integer $position (optional)
        Example    :  my $position=$probe->mismatch_position();
     Description: 	Get/set the postition of the mismatch base (in the
     25-mer oligo. As far as the author knows, all factory Affymetrix
    chips have the mismatch probe in position 13).
        Returntype : integer
        Exceptions : none
        Caller     : general

new | code | top | prev | next

      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

original_probepair_number | code | top | prev | next

        Arg [0]    : none
        Example    : my $original_number=$probe->original_probepair_number();
      Description: 	Returns the probe pair number as written in the file
        Returntype : integer $number
        Exceptions : none
        Caller     : general

original_probeset | code | top | prev | next

        Arg [0]    : none
        Example    : my $name=$probe->original_probeset()
      Description: 	The name of the original probeset this probe came from
        Returntype : string $probesetname
        Exceptions : none
        Caller     : general

probe_mismatch_base(2) | code | top | prev | next

        Arg [1]    : char $base
        Example    : my $base=$probe->probe_target_base()
      Description: 	Get/set what the base (A, C, T or G) would be if it is to detect for
        the target sequence. Non-mismatch probes have
        probe_mismatch_base() eq probe_target_base().
        Returntype : char $base
        Exceptions : none
        Caller     : general

x | code | top | prev | next

        Arg [1]    :  integer $x (optional)
        Example    :  my $x=$probe->x();
     Description: 	Get/set the y coordinate of this probe
        Returntype : integer
        Exceptions : none
        Caller     : general

y | code | top | prev | next

        Arg [1]    : 	integer $y (optional)
        Example    : 	my $name=$probe->cols()
      Description: 	Get/set the y coordinate of this probe
        Returntype : integer
        Exceptions : none
        Caller     : general

## Methods code

index | description | top | prev | next

sub index {

        my $self=shift;

        if (my $q=shift) {
    	$self->{"INDEX"}=$q;
        }
        return $self->{"INDEX"};

}

is_mismatch | description | top | prev | next

sub is_mismatch {

        my $self=shift;
        return !($self->probe_target_base() eq $self->probe_mismatch_base());

}

mismatch_position | description | top | prev | next

sub mismatch_position {

        my $self=shift;

        if (my $q=shift) {
    	$self->{"POS"}=$q;
        }

        return $self->{"POS"};

}

new | description | top | prev | next

sub new {

        my $class=shift;
        my $q=shift;
        my $self={};

        bless $self,$class;

        return $self;

}

original_probe_number | description | top | prev | next

sub original_probe_number {

        my $self=shift;
        return $self->{"EXPOS"};

}

original_probepair_number | description | top | prev | next

sub original_probepair_number {

        my $self=shift;

        return $self->{"ATOM"};

}

original_probeset | description | top | prev | next

sub original_probeset {

        my $self=shift;
        return $self->{"PROBESET"};

}

probe_mismatch_base | description | top | prev | next

sub probe_mismatch_base {

        my $self=shift;

        if (my $q=shift) {
    	$self->{"PBASE"}=$q;
        }

        return $self->{"PBASE"};

}

probe_target_base | description | top | prev | next

sub probe_target_base {

        my $self=shift;

        if (my $q=shift) {
    	$self->{"TBASE"}=$q;
        }

        return $self->{"TBASE"};

}

x | description | top | prev | next

sub x {

        my $self=shift;

        if (my $q=shift) {
    	$self->{"X"}=$q;
        }

        return $self->{"X"};

}

y | description | top | prev | next

sub y {

        my $self=shift;

        if (my $q=shift) {
    	$self->{"Y"}=$q;
        }

        return $self->{"Y"};

}

## General documentation

COPYRIGHT | top
    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.
AUTHORS | top
    Nick James (nick at arabidopsis.info)

    David J Craigon (david at arabidopsis.info)

    Nottingham Arabidopsis Stock Centre (http://arabidopsis.info), University of Nottingham.
orignal_probe_number | top
        Arg [0]    : none
        Example    : my $position=$probe->original_probe_number()
      Description: 	The name of the original index of this probe in the probeset
        Returntype : string $probesetname
        Exceptions : none
        Caller     : general