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Harshlight | A "corrective make-up" program for microarray chips


A package for the automatic detection and masking of blemishes in HDONA microarray chips. Harshlight’s algorithm combines image analysis techniques with statistical approaches to recognize three types of defects frequent in Affymetrix microarray chips: extended, compact, and diffuse defects. It provides a way to safely identify blemishes of different nature and correct the intensity values of the batch of chips provided by the user. The corrections made by Harshlight improve the reliability of the expression values when the chips are further analyzed with other programs, such as GCRMA and MAS5.

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Harshlight classification

Harshlight specifications

Unique identifier:
Command line interface
Operating system:
Unix/Linux, Mac OS, Windows
GNU General Public License version 2.0
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Harshlight distribution


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Center for Studies in Physics and Biology, The Rockefeller University, New York, NY, USA

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