Optimal factorial designs for CDNA microarray experiments

DOI10.1214/07-AOAS144SUPPzbMATH Open1137.62074arXiv0803.3911MaRDI QIDQ2482985FDOQ2482985

Authors: Rahul Mukerjee, Tathagata Banerjee 

Publication date: 30 April 2008

Published in: The Annals of Applied Statistics (Search for Journal in Brave)

Abstract: We consider cDNA microarray experiments when the cell populations have a factorial structure, and investigate the problem of their optimal designing under a baseline parametrization where the objects of interest differ from those under the more common orthogonal parametrization. First, analytical results are given for the $2imes2$ factorial. Since practical applications often involve a more complex factorial structure, we next explore general factorials and obtain a collection of optimal designs in the saturated, that is, most economic, case. This, in turn, is seen to yield an approach for finding optimal or efficient designs in the practically more important nearly saturated cases. Thereafter, the findings are extended to the more intricate situation where the underlying model incorporates dye-coloring effects, and the role of dye-swapping is critically examined.

Full work available at URL: https://arxiv.org/abs/0803.3911

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zbMATH Keywords

interactionadmissibilityweighted optimalitysaturated designmain effectaugmented designorthogonal parametrizationbaseline parametrizationdye-swapping

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Optimal statistical designs (62K05) Factorial statistical designs (62K15) Biochemistry, molecular biology (92C40)

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Cited In (17)

• Optimal biased weighing designs and two-level main-effect plans
• A systematic construction of compromise designs under baseline parameterization
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• Sequential Design for Microarray Experiments
• Compromise designs under baseline parameterization
• Selecting baseline designs using a minimum aberration criterion when some two-factor interactions are important
• Balanced Factorial Designs for cDNA Microarray Experiments
• Approximate theory-aided robust efficient factorial fractions under baseline parametrization
• Factorial and time course designs for cDNA microarray experiments
• Experimental design for gene expression microarrays
• Robust multistratum baseline designs
• Experimental designs for 2‐colour cDNA microarray experiments
• Efficient design and analysis of two colour factorial microarray experiments
• Relationship between orthogonal and baseline parameterizations and its applications to design constructions
• Highly efficient factorial designs for cDNA microarray experiments: use of approximate theory together with a step-up step-down procedure
• Algorithmic search for baseline minimum aberration designs
• Optimal factorial designs for CDNA microarray experiments

Uses Software

• daMA

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