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Bioinformatics Advance Access published online on July 26, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti576
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received May 12, 2005
Revised July 5, 2005
Accepted July 6, 2005

Applications note

Automated microarray image analysis toolbox for MATLAB

Amanda M. White 1*, Don S. Daly 1, Alan R. Willse 1, Miroslava Protic 2, and Darrell P. Chandler 2

1 Statistical Sciences, Pacific Northwest National Laboratory, Richland, WA 99352
2 Biochip Technology Center, Argonne National Laboratory, Argonne, IL 60439

* To whom correspondence should be addressed.
Amanda M. White, E-mail: amanda.white{at}pnl.gov


  Abstract

Summary: The Automated Microarray Image Analysis (AMIA) Toolbox for MATLAB is a flexible, open-source, microarray image analysis tool that allows the user to customize analyses of microarray image sets. This tool provides several methods to identify and quantify spot statistics, as well as extensive diagnostic statistics and images to evaluate data quality and array processing. The open, modular nature of AMIA provides access to implementation details and encourages modification and extension of AMIA's capabilities.

Availability: The AMIA Toolbox is freely available at http://www.pnl.gov/statistics/amia. The AMIA Toolbox requires MATLAB 6.5 (R13) (MathWorks, Inc. Natick, MA), as well as the Statistics Toolbox 4.1 and Image Processing Toolbox 4.1 for MATLAB or more recent versions.


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