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Bioinformatics Vol. 18 no. 5 2002
Pages 771-773
© 2002 Oxford University Press

Applications Note

GP3: GenePix post-processing program for automated analysis of raw microarray data

M. R. Fielden , R. G. Halgren , E. Dere and T. R. Zacharewski

Department of Biochemistry & Molecular Biology, National Food Safety & Toxicology Center, Institute for Environmental Toxicology, Michigan State University, East Lansing, MI 48824, USA

Received on October 7, 2001 ; revised on November 22, 2001 and December 19, 2001 ; accepted on December 21, 2001

Summary: Here we describe an automated and customizable program to correct, filter and normalize raw microarray data captured using GenePix, a commonly used microarray image analysis application. Files can be processed individually or in batch mode for increased throughput. User defined inputs specify the stringency of data filtering and the method and conditions of normalization. The output includes gene summaries for replicate spots and descriptive statistics for each experiment. The source code (Perl) can also be adapted to handle raw data output from other image analysis applications.

Availability: http://bch.msu.edu/~zacharet/microarray/GP3.html

Contact: tzachare{at}msu.edu

Supplementary information: http://bch.msu.edu/~zacharet/microarray/GP3.html

* To whom correspondence should be addressed.


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