Module detail: CEL.pm

NAME

ArrayExpress::Datafile::Affymetrix::CEL.pm - CEL data file parsing

SYNOPSIS

 use ArrayExpress::Datafile::Affymetrix::CEL;

 my $cel = ArrayExpress::Datafile::Affymetrix::CEL->new({
     input => 'mydatafile.CEL',
 });
 $cel->parse();
 $cel->export($output_fh);

This module implements an abstract superclass used in parsing and export of data from Affymetrix CEL files.

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

parse_header(): This method will take the input attribute and parse only the header metadata. Note that for older CEL file formats, the numbers of masked, outlier or modified cells are not set by this method, since these values are embedded in the main body of the data.
export($fh): This method takes a filehandle and prints the parsed expression data out to it. The QuantitationTypeDimension and DesignElementDimension of the resulting matrix are given by the get_qtd and get_ded methods, respectively.
get_ded($chip_type): This method takes an optional string argument representing the chip type (e.g., ``HG-U133A'') and uses it to generate a reference to an array of Feature 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 $cel->get_chip_type() method is used to derive a value; note however that that method relies on parsing an undocumented tag and as such it may fail.
get_num_masked(): The number of masked cells.
get_num_outliers(): The number of outlier cells.
get_num_modified(): The number of modified cells (this should always be zero).

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.