Bio::Affymetrix::CEL- parse Affymetrix CEL files
use Bio::Affymetrix::CEL;
# Parse the CDF file
my $cel=new Bio::Affymetrix::CEL();
$cel->parse_from_file("foo.cel");
# Print out all of the intensities for each square
for (my $x=0;$x<scalar(@{$cel->intensity_map()});$x++) { for (my $y=0;$y<scalar(@{cel->intensity_map()->[$x]});$y++) { print join(",",($x,$y,$cel->intensity_map->[$x][$y]->[0])."\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 CEL files. Use this module if you want to find out about the results for individual probes on an array.
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 takes lots of memory due to the way Perl stores arrays. If you are writing a program that uses many CEL files, delete each CEL file once you have the information you need from it.
You fill the object filled with data using the parse_from_filehandle, parse_from_string or parse_from_file routines. You can get/set various statistics using methods on the object.
The key method is intensity_map. This returns a reference to a 2D array of parameters for each square.
Modules were written with the official Affymetrix documentation, which can be located at http://www.affymetrix.com/support/developer/AffxFileFormats.ZIP
This module can parse the CEL files produced by the Affymetrix software MAS 5 and GCOS.
Writing CEL files as well as reading them.
Copyright (C) 2005 by Nick James, David J Craigon, NASC, The University of Nottingham
This module is free software. You can copy or redistribute it under the same terms as Perl itself.
Affymetrix is a registered trademark of Affymetrix Inc., Santa Clara, California, USA.
Nick James (nick at arabidopsis.info)
David J Craigon (david at arabidopsis.info)
Nottingham Arabidopsis Stock Centre (http://arabidopsis.info), University of Nottingham.
Arg [0] : none Example : my $cel=new Bio::Affymetrix::CEL(); Description: constructor for CEL object Returntype : new Bio::Affmetrix::CEL object Exceptions : none Caller : general
Arg [0] : none Example : my $cel_file_name=$cel->original_file_name(); Description: If this object was created using parse_from_file, the original filename. Otherwise undef. Returntype : string Exceptions : none Caller : general
Arg [1] : string $algorithm_name (optional) Example : my $algorithm_name=$cel->algorithm_name(); Description: Get/set the algorithm name that created this CEL file. Returntype : string Exceptions : none Caller : general
Arg [1] : hashref $algorithm_params (optional) Example : my %algorithm_params=%{$cel->algorithm_params()};
# Print margin of cells ignored for calculating signal
print $algorithm_params("CellMargin");
Description: Get/set the algorithm parameters for the CEL file creation Returntype : hashref Exceptions : none Caller : general
Arg [1] : string Example : $cel->parse_from_string($cel_file_in_a_string); Description: Parse a CEL file from a buffer in memory Returntype : none Exceptions : none Caller : general
Arg [1] : string Example : $cel->parse_from_file($cel_filename); Description: Parse a CEL file from a file Returntype : none Exceptions : dies if cannot open file Caller : general
Arg [1] : reference to filehandle Example : $cel->parse_from_filehandle(\*STDIN); Description: Parse a CEL file from a filehandle Returntype : none Exceptions : none Caller : general
To install Bio::Affymetrix::CEL, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Affymetrix::CEL
CPAN shell
perl -MCPAN -e shell install Bio::Affymetrix::CEL
For more information on module installation, please visit the detailed CPAN module installation guide.