Module detail: Affymetrix/Parser.pm

NAME

ArrayExpress::Datafile::Affymetrix::Parser - an Affymetrix data file parsing module.

SYNOPSIS

 use base qw( ArrayExpress::Datafile::Affymetrix::Parser );

DESCRIPTION

This module is an abstract superclass used in the parsing and export of data from Affymetrix file formats. CEL, CHP and EXP formats are supported, with limited CDF parsing. Both old (GDAC) and new (GCOS/XDA) file formats can be parsed.

There is a set of methods common to all the Affymetrix file classes, listed below. There are additional methods, specific to each class, which are documented in the relevant pages.

METHODS

The following methods are common to all classes.

new({ input => 'myfile.CEL' })

The class constructor. This method returns a an object of the appropriate class, without performing any additional processing.

parse()

This method will take the value for the input attribute and parse the data into memory so that it can be interrogated using the methods below.

Accessor methods

Each of these methods acts as both setter and getter for the attributes in question. Typically these will be used to access the data and metadata which was extracted using the parse method. Please see the respective subclass documentation for information on the export and get_ded methods. Note that many of the following will have no meaning for EXP file metadata.

get_version()

The version number or string associated with the file. For CEL and CHP files this should be either 3 or 4.

get_num_columns()

The number of columns on the array.

get_num_rows()

The number of rows on the array.

get_num_cells()

The number of cells on the array. For CEL files this corresponds to the number of columns multiplied by the number of rows.

get_algorithm()

The name of the algorithm used to produce the data (e.g. ``Percentile'', ``ExpressionStat'').

get_chip_type()

The type of chip used (e.g., HG-U133A). This is supported for EXP files, CEL files, CHP files and GDAC format CDF files. Note that for CEL files this relies on parsing a header tag which is not actually documented by Affymetrix, and so it is possible that this method is not to be trusted in such cases.

get_parameters()

A reference to a hash with parameter {name => value} pairs. Parameters are grouped as follows:

 CEL: Feature extraction parameters
 CHP: Normalization parameters
 EXP: Hybridization parameters (numbered).

get_stats()

A reference to a hash with statistic {name => value} pairs. Statistics are grouped as follows:

 CEL: Feature extraction summary statistics
 CHP: Normalization summary statistics

get_qtd()

A reference to an array listing the QuantitationType identifiers (long form) in the column order that they are output by the export method. See also the headings method below.

get_headings()

A reference to an array listing the QuantitationType names (short form) in the column order that they are output by the export method. Using this method also populates the qtd method data structure, but not vice versa.

AUTHOR

Tim Rayner (rayner@ebi.ac.uk), ArrayExpress team, EBI, 2005.

Acknowledgements go to the ArrayExpress curation team for feature requests, bug reports and other valuable comments.