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Bioinformatics Vol. 17 no. 90001 2001
Pages S323-S331
© 2001 Oxford University Press

Centralization: a new method for the normalization of gene expression data

Alexander Zien , Thomas Aigner , Ralf Zimmer and Thomas Lengauer

SCAI - Institute for Algorithms and Scientific Computing, GMD - German National Research Center for Information Technology, Schloss Birlinghoven, Sankt Augustin, 53754, Germany
2 Department of Pathology, University of Erlangen-Nürnberg, Krankenhausstr. 8-10, Erlangen, 91054, Germany

Received on February 5, 2001 ; revised on March 30, 2001 ; accepted on March 30, 2001

Microarrays measure values that are approximately proportional to the numbers of copies of different mRNA molecules in samples. Due to technical difficulties, the constant of proportionality between the measured intensities and the numbers of mRNA copies per cell is unknown and may vary for different arrays. Usually, the data are normalized (i.e., array-wise multiplied by appropriate factors) in order to compensate for this effect and to enable informative comparisons between different experiments. Centralization is a new two-step method for the computation of such normalization factors that is both biologically better motivated and more robust than standard approaches. First, for each pair of arrays the quotient of the constants of proportionality is estimated. Second, from the resulting matrix of pairwise quotients an optimally consistent scaling of the samples is computed.

Contact: Alexander.Zien{at}gmd.de


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