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Bioinformatics Advance Access published online on August 9, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl434
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© 2006 The Author(s)
Received May 29, 2006
Revised July 7, 2006
Accepted August 4, 2006

Applications note

MASQOT-GUI: spot quality assessment for the two-channel microarray platform

Max Bylesjö 1 *, Andreas Sjödin 2, Daniel Eriksson 3, Henrik Antti 1, Thomas Moritz 3, Stefan Jansson 2, and Johan Trygg 1

1 Research group for Chemometrics, Department of Chemistry, Umeå University, SE-901 87 Umeå, Sweden
2 Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden
3 Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden

* To whom correspondence should be addressed.
Max Bylesjö, E-mail: max.bylesjo{at}chem.umu.se


  Abstract

Summary: MASQOT-GUI provides an open-source, platform-independent software pipeline for two-channel microarray spot quality control. This includes gridding, segmentation, quantification, quality assessment and data visualization. It hosts a set of independent applications, with interactions between the tools as well as import and export support for external software. The implementation of automated multivariate quality control assessment, which is a unique feature of MASQOT-GUI, is based on the previously documented and evaluated MASQOT methodology (Bylesjö, et al., 2005). Further abilities of the application are outlined and illustrated.

Availability: MASQOT-GUI is Java-based and licensed under the GNU Lesser General Public License (LGPL). Source code, documentation and binary files for the Windows and Linux platforms are available for download at http://masqot-gui.sourceforge.net/.

Associate Editor: Joaquin Dopazo
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