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Bioinformatics Advance Access published online on March 18, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn085
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

A suite of Perl modules for handling Microarray data

James A Morris 1, Simon A Gayther 1, Ian J Jacobs 1 and Christopher Jones 1,*

1Translational Research Laboratories, UCL EGA Institute for Women's HealthInstitute for Women's Health, University College London, United Kingdom

*To whom correspondence should be addressed. Jimin Pei, E-mail: jpei{at}chop.swmed.edu


  Abstract

Summary: We describe PerlMAT, a Perl microarray toolkit providing easy to use object-oriented methods for the simplified manipulation, management and analysis of microarray data. The toolkit provides objects for the encapsulation of microarray spots and reportersfeatures, several common microarray data file formats and GAL files. In addition, an analysis object provides methods for data processing, and an image object enables the visualisation of microarray data. This important addition to the Perl developer's library will facilitate more widespread use of Perl for microarray application development within the bioinformatics community. The coherent interface and well documented code enables rapid analysis by even inexperienced Perl developers.

Availability: http://sourceforge.net/projects/perlmat

Contact: c.jones{at}ucl.ac.uk

Associate Editor: Prof. John Quackenbush

Received on December 14, 2007; revised on February 14, 2008; accepted on March 1, 2008

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