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Briefings in Bioinformatics 2005 6(2):135-145; doi:10.1093/bib/6.2.135
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© Henry Stewart Publications

Combining microarrays and genetic analysis

Rudi Alberts *
PhD Student at the Groningen Bioinformatics Centre of the University of Groningen, focusing on genetical genomics in the mouse.

Jingyuan Fu *
PhD student at the Groningen Bioinformatics Centre of the University of Groningen, focusingongenetical genomics in Arabidopsis.

Morris A. Swertz
PhD student at the Groningen Bioinformatics Centre of the University of Groningen, focusing on information systems in the life sciences. He has developed an information system for microarray data by using advanced code generation technologies.

L. Alrik Lubbers
Works at the Groningen Bioinformatics Centre of the University of Groningen as a software engineer, specialising on automatic code generation for information systems in the life sciences.

Casper J. Albers
Works at the Groningen Bioinformatics Centre of the University of Groningen on the statistical analysis of bioinformatics data, in particular, microarray data.

Ritsert C. Jansen
Leads the Groningen Bioinformatics Centre of the University of Groningen with research on statistics, information analysis and system development for ‘omics’ data.


Ritsert C. Jansen, Groningen Bioinformatics Centre, Kerklaan 30, 9751 NN, Haren, the Netherlands Tel: +31 50 3638089 Fax: +31 50 3633400 E-mail: r.c.jansen{at}rug.nl

Gene expression can be studied at a genome-wide scale with the aid of modern microarray technologies. Expression profiling of tens to hundreds of individuals in a genetic population can reveal the consequences of genetic variation. In this paper it is argued that the design and analysis of such a study is not a matter of simply applying the existing and more-or-less standard computational tools for microarrays to a new type of experimental data. It is shown how to fully exploit the power of genetics through optimal experimental design and analysis for two major microarray technologies, cDNA two-colour arrays and Affymetrix short oligonucleotide arrays.

Keywords: microarray, gene expression, quantitative trait locus, QTL, two-colour microarray, oligonucleotide microarray

*The authors have contributed equally to this paper


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