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Journal of Computational Biology
Microarrays: How Many Do You Need?
To cite this article:
Alexander Zien, Juliane Fluck, Ralf Zimmer, Thomas Lengauer.
Journal of Computational Biology.
June 2003,
10(3-4): 653-667.
doi:10.1089/10665270360688246.
Alexander Zien Max-Planck-Institut für biologische Kybernetik, Spemannstrasse 38, 72076 Tübingen, Germany Juliane Fluck Fraunhofer-Institut für Algorithmen und Wissenschaftliches Rechnen SCAI, Schloss Birlinghoven, 53754 Sankt Augustin, Germany and (current address): Institut für Informatik der LMU, Theresienstrasse 39, 80333 München, Germany and (current address): Max-Planck-Institut für Informatik, Stuhlsatzenhausweg 85, 66123 Saarbrücken, Germany Ralf Zimmer Fraunhofer-Institut für Algorithmen und Wissenschaftliches Rechnen SCAI, Schloss Birlinghoven, 53754 Sankt Augustin, Germany and (current address): Institut für Informatik der LMU, Theresienstrasse 39, 80333 München, Germany and (current address): Max-Planck-Institut für Informatik, Stuhlsatzenhausweg 85, 66123 Saarbrücken, Germany Thomas Lengauer Fraunhofer-Institut für Algorithmen und Wissenschaftliches Rechnen SCAI, Schloss Birlinghoven, 53754 Sankt Augustin, Germany and (current address): Institut für Informatik der LMU, Theresienstrasse 39, 80333 München, Germany and (current address): Max-Planck-Institut für Informatik, Stuhlsatzenhausweg 85, 66123 Saarbrücken, Germany We estimate the number of microarrays that is required in order to gain reliable results from a common type of study: the pairwise comparison of different classes of samples. We show that current knowledge allows for the construction of models that look realistic with respect to searches for individual differentially expressed genes and derive prototypical parameters from real data sets. Such models allow investigation of the dependence of the required number of samples on the relevant parameters: the biological variability of the samples within each class, the fold changes in expression that are desired to be detected, the detection sensitivity of the microarrays, and the acceptable error rates of the results. We supply experimentalists with general conclusions as well as a freely accessible Java applet at www.scai.fhg.de/special/bio/howmanyarrays/ for fine tuning simulations to their particular settings.  This paper was cited by:PDK-1 regulates lactate production in hypoxia and is associated with poor prognosis in head and neck squamous cancer S M Wigfield, S C Winter, A Giatromanolaki, J Taylor, M L Koukourakis, A L Harris British Journal of Cancer. Jul 2008, Vol. 98, No. 12: 1975-1984 CrossRef EVE (external variance estimation) increases statistical power for detecting differentially expressed genes Anja Wille, Wilhelm Gruissem, Peter Bühlmann, Lars Hennig The Plant Journal. Dec 2007, Vol. 52, No. 3: 561-569 CrossRef Associating phenotypes with molecular events: recent statistical advances and challenges underpinning microarray experiments Yulan Liang, Arpad Kelemen Functional & Integrative Genomics. Feb 2006, Vol. 6, No. 1: 1-13 CrossRef Microarray data analysis: from disarray to consolidation and consensus David B. Allison, Xiangqin Cui, Grier P. Page, Mahyar Sabripour Nature Reviews Genetics. Feb 2006, Vol. 7, No. 1: 55-65 CrossRef Kidney Transplant Rejection and Tissue Injury by Gene Profiling of Biopsies and Peripheral Blood Lymphocytes Stuart M. Flechner, Sunil M. Kurian, Steven R. Head, Starlette M. Sharp, Thomas C. Whisenant, Jie Zhang, Jeffrey D. Chismar, Steve Horvath, Tony Mondala, Timothy Gilmartin, Daniel J. Cook, Steven A. Kay, John R. Walker, Daniel R. Salomon American Journal of Transplantation. Oct 2004, Vol. 4, No. 9: 1475-1489 CrossRef Correlated stage- and subfield-associated hippocampal gene expression patterns in experimental and human temporal lobe epilepsy Albert J. Becker, Jian Chen, Alexander Zien, Dmitry Sochivko, Sabine Normann, Johannes Schramm, Christian E. Elger, Otmar D. Wiestler, Ingmar Blumcke European Journal of Neuroscience. Dec 2003, Vol. 18, No. 10: 2792-2802 CrossRef |
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