/ 
bioperl-microarray-0.1
/ Bio::Expression::MicroarrayIO::affymetrix

NAME

Bio::Expression::MicroarrayIO::affymetrix - Work with an Affymetrix array.

SYNOPSIS

  $stream  = Bio::Expression::MicroarrayIO->new(
		'-file'     => "my.cel",
		'-template' => "my.cdf",
		'-format'   => "affymetrix",
						);

DESCRIPTION

Bio::Expression::MicroarrayIO::affymetrix parses Affymetrix CEL files in the context of a CDF file.

FEEDBACK

Direct feedback to <allenday@ucla.edu> or to the Bioperl mailing list (see below).

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.

bioperl-l@bioperl.org            - General discussion
http://bioperl.org/MailList.shtml - About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web:

bioperl-bugs@bio.perl.org
http://bio.perl.org/bioperl-bugs/

AUTHOR

Allen Day <allenday@ucla.edu>

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

 Title   : new
 Usage   : Bio::Expression::MicroarrayIO::affymetrix->new(
											  -file     => 'path/to/filename',
											  -template => 'path/to/template')
 Comments: You should probably not be instantiating this module directly.
           Use MicroarrayIO instead.
 Args    : -file     => filename
           -format   => format
           -template => template

_initialize

 Title   : _initialize
 Usage   : $affy->_initialize(
							  -file     => 'path/to/filename',
							  -template => 'path/to/template'
							 );
 Function: Loads up a template module that will be used to
           by next_array();
 Returns : nothing.
 Args    : -file     => filename
           -format   => format
           -template => template

templatefile

Title   : templatefile
Usage   : $affy->templatefile('path/to/template');
          $affy->templatefile();
Function: get/set the the location of a template file
Returns : path to a template file
Args    : optional path to a template file

datafile

Title   : datafile
Usage   : $affy->datafile('path/to/datafile');
          $affy->datafile();
Function: get/set the the location of a data file
Returns : path to a data file
Args    : optional path to a data file

array

Title   : array
Usage   : $affy->array($template);
          $affy->array();
Comments: You probably should not be using this method
          to set the array template object.  Use load_array() instead.
Function: get/set the the array template object
Returns : a Bio::Expression::Microarray::Affymetrix::ArrayDesign object
Args    : optional Bio::Expression::Microarray::Affymetrix::ArrayDesign object

load_array

Title   : load_array
Usage   : $affy->load_array($template);
          $affy->load_array();
Function: cause a Bio::Expression::Microarray::Affymetrix::ArrayDesign
          object to be created using $affy->templatefile().
Returns : a  Bio::Expression::Microarray::Affymetrix::ArrayDesign object
Args    : optional path to a template file, which is stored in
          $affy->templatefile before the Template object is created.

next_array

Title   : next_array
Usage   : $affy->next_array();
Function: reads an Affymetrix data record from $affy->datafile
Returns : a loaded array object
Args    : none

write_array

Title   : write_array
Usage   : $affy->write_array($array);
Function: write an Affymetrix data record using $array
Returns : nothing.  prints a lot of text to the MicroarrayIO stream.
Args    : A Bio::Expression::MicroarrayI compliant object.