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December 2009 Inference on low-rank data matrices with applications to microarray data
Xingdong Feng, Xuming He
Ann. Appl. Stat. 3(4): 1634-1654 (December 2009). DOI: 10.1214/09-AOAS262


Probe-level microarray data are usually stored in matrices, where the row and column correspond to array and probe, respectively. Scientists routinely summarize each array by a single index as the expression level of each probe set (gene). We examine the adequacy of a unidimensional summary for characterizing the data matrix of each probe set. To do so, we propose a low-rank matrix model for the probe-level intensities, and develop a useful framework for testing the adequacy of unidimensionality against targeted alternatives. This is an interesting statistical problem where inference has to be made based on one data matrix whose entries are not i.i.d. We analyze the asymptotic properties of the proposed test statistics, and use Monte Carlo simulations to assess their small sample performance. Applications of the proposed tests to GeneChip data show that evidence against a unidimensional model is often indicative of practically relevant features of a probe set.


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Xingdong Feng. Xuming He. "Inference on low-rank data matrices with applications to microarray data." Ann. Appl. Stat. 3 (4) 1634 - 1654, December 2009.


Published: December 2009
First available in Project Euclid: 1 March 2010

zbMATH: 1184.62182
MathSciNet: MR2752151
Digital Object Identifier: 10.1214/09-AOAS262

Keywords: hypothesis test , microarray , Singular value decomposition

Rights: Copyright © 2009 Institute of Mathematical Statistics


Vol.3 • No. 4 • December 2009
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