Bio::Affymetrix::CDF 0.5

Bio::Affymetrix::CDF is a Perl module to parse Affymetrix CDF files.

SYNOPSIS

use Bio::Affymetrix::CDF;

# Parse the CDF file

my $cdf=new Bio::Affymetrix::CDF({"probemode"=>0});

$cdf->parse_from_file("foo.cdf");

# Find some fun facts about this chip type

print $cdf->rows().",".$cdf->cols()."n";

print $cdf->version()."n";

# Print out all of the probeset names on this chip type

foreach my $i (keys %{$chp->probesets}) { print $chp->probesets->{$i}->name()."n"; }

The Affymetrix microarray system produces files in a variety of formats. If this means nothing to you, these modules are probably not for you :). This module parses CDF files. Use this module if you want to find out about the design of an Affymetrix GeneChip, or you need the object for another one of the modules in this package.

All of the Bio::Affymetrix modules parse a file entirely into memory. You therefore need enough memory to hold these objects. For some applications, parsing as a stream may be more appropriate- hopefully the source to these modules will give enough clues to make this an easy task. This module in particular takes a lot of memory if probe information is also stored (about 150Mb). Memory usage is not too onorous (about 15Mb) if probe level information is omitted. You can.control this by setting probemode=>1 or probemode=>0 in the constructor.

You can also use these modules to write CDF files (using the write_to_filehandle method). See COMPATIBILITY for some important caveats.

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Requirements:

· Perl