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

NAME

Bio::Expression::MicroarrayIO::dchipxls - Work with dChip analysis of an Affymetrix array.

SYNOPSIS

  $stream  = Bio::Expression::MicroarrayIO->new(
		'-file'     => "my.xls",
		'-format'   => "dchipxls",
											   );

DESCRIPTION

Bio::Expression::MicroarrayIO::dchipxls parses dChip XLS files. These are a processed (normalized) form of Affymetrix CEL files using the algorithm described in: Li C, Hung Wong W. Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application. Genome Biol. 2001;2(8)

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   : new
 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

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

next_array

Title   : next_array
Usage   : $affy->next_array();
Function: reads an Affymetrix data record from $affy->datafile
Returns : a  Bio::Expression::Microarray::Affymetrix::Template object
          that has been filled with probe values.
Args    :

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.
Args    : A Bio::Expression::MicroarrayI compliant object.