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reproducibility assessment of independent component analysis of expression ratios from dna microarrays独立分量分析的重现性评估从dna微阵列表达率.pdf

reproducibility assessment of independent component analysis of expression ratios from dna microarrays独立分量分析的重现性评估从dna微阵列表达率.pdf

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reproducibility assessment of independent component analysis of expression ratios from dna microarrays独立分量分析的重现性评估从dna微阵列表达率

Comparative and Functional Genomics Comp Funct Genom 2003; 4: 300–317. Published online in Wiley InterScience (). DOI: 10.1002/cfg.298 Primary Research Paper Reproducibility assessment of independent component analysis of expression ratios from DNA microarrays David Philip Kreil1,2* and David J. C. MacKay2 1Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK 2 Inference Group, Cavendish Laboratory, Madingley Road, Cambridge CB3 0HE, UK *Correspondence to: Abstract David Philip Kreil, Department of Genetics, University of DNA microarrays allow the measurement of transcript abundances for thousands Cambridge, Downing Street, of genes in parallel. Most commonly, a particular sample of interest is studied next Cambridge CB2 3EH, UK. to a neutral control, examining relative changes (ratios). Independent component E-mail: kreil@ebi.ac.uk analysis (ICA) is a promising modern method for the analysis of such experiments. The condition of ICA algorithms can, however, depend on the characteristics of the data examined, making algorithm properties such as robustness specific to the given application domain. To address the lack of studies examining the robustness of ICA applied to microarray measurements, we report on the stability of variational Bayesian ICA in this domain. Microarray data are usually preprocessed and transformed. Hence we first examined alternative transforms and data selections for the smallest modelling reconstruction errors. Log-ratio data a

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