Tab2MAGE logo Module detail: CHP.pm

NAME

ArrayExpress::Datafile::Affymetrix::CHP - GDAC CHP data file parsing.


SYNOPSIS

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

DESCRIPTION

Abstract superclass for parsing and export of data from Affymetrix CHP files.

Please see the the ArrayExpress::Datafile::Affymetrix::Parser manpage documentation for methods common to all the Affymetrix file classes.


METHODS

parse_header()

This method will take the input attribute and parse only the header metadata.

export($fh, $cdf)

This method takes a filehandle and prints the parsed expression data out to it. The method also requires a pre-parsed CDF object to be passed to it. The QuantitationTypeDimension and DesignElementDimension of the resulting matrix are given by the get_qtd and get_ded methods, respectively.

get_ded($cdf, $chip_type)

This method takes a pre-parsed CDF object, and an optional string argument representing the chip type (e.g., ``HG-U133A''). The method uses these arguments to generate a reference to an array of CompositeSequence identifiers, arranged in the order that the export method outputs them (i.e., a DesignElementDimension). The chip type can be derived in a number of ways; if EXP files are available, for instance, the $exp->get_chip_type() method should return an appropriate string. If this argument is not supplied then the chip_type() methods for the CHP and CDF objects are inspected.


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.


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