ArrayExpress::Datafile::Affymetrix::CHP - GDAC CHP data file parsing.
use base qw( ArrayExpress::Datafile::Affymetrix::CHP );
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.
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.
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.