Profound effect of normalization on detection of differentially expressed genes in oligonucleotide microarray data analysis 英文参考文献.docVIP

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Profound effect of normalization on detection of differentially expressed genes in oligonucleotide microarray data analysis 英文参考文献.doc

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Profound effect of normalization on detection of differentially expressed genes in oligonucleotide microarray data analysis 英文参考文献

/2002/3/7/research/0033.1 Research Profound effect of normalization on detection of differentially expressed genes in oligonucleotide microarray data analysis Reinhard Hoffmann*, Thomas Seidl? and Martin Dugas? Addresses: *Department of Bacteriology, Max von Pettenkofer Institut, Pettenkoferstrasse 9a, 80336 Munich, Germany. ?Section of Gene -unction and Regulation, Institute of Cancer Research, Chester Beatty Laboratories, 237 -ulham Road, London SW3 6JB, UK. ?Department of Medical Informatics, Biometrics and Epidemiology, University of Munich, Marchioninistrasse 15, 81377 Munich, Germany. Correspondence: Reinhard Hoffmann. E-mail: r_hoffmann@m3401.mpk.med.uni-muenchen.de Published: 14 June 2002 Received: 7 February 2002 Revised: 4 April 2002 Accepted: 24 April 2002 GenomeBiology 2002, 3(7):research0033.1–0033.11 The electronic version of this article is the complete one and can be found online at /2002/3/7/research/0033 ? 2002 Hoffmann et al., licensee BioMed Central Ltd (Print ISSN 1465-6906; Online ISSN 1465-6914) Abstract Background: Oligonucleotide microarrays measure the relative transcript abundance of thousands of mRNAs in parallel. A large number of procedures for normalization and detection of differentially expressed genes have been proposed. However, the relative impact of these methods on the detection of differentially expressed genes remains to be determined. Results: We have employed four different normalization methods and all possible combinations with three different statistical algorithms for detection of differentially expressed genes on a prototype dataset. The number of genes detected as differentially expressed differs by a factor of about three. Analysis of lists of genes detected as differentially expressed, and rank correlation coefficients for probability of differential expression shows that a high concordance between different methods can only be achieved by