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Title: An experimental evaluation of a loop versus a reference design for two-channel microarrays
Authors: Vinciotti, V
Khanin, R
D'Alimonte, D
Liu, X
Cattini, N
Hotchkiss, G
de Jesus, O
Rasaiyaah, J
Smith, C P
Kellam, P
Wit, E
Issue Date: 2004
Publisher: Oxford University Press
Citation: Oxford Journals Life Sciences Bioinformatics Volume 21, Number 4 Pp. 492-501
Abstract: Motivation: Despite theoretical arguments that socalled \loop designs" of two-channel DNA microarray experiments are more e cient, biologists keep on using \reference designs". We describe two sets of microarray experiments with RNA from two di erent biological systems (TPA-stimulated mammalian cells and Streptomyces coelicor). In each case, both a loop and a reference design were performed using the same RNA preparations with the aim to study their relative e ciency. Results: The results of these experiments show that (1) the loop design attains a much higher precision than the reference design, (2) multiplicative spot effects are a large source of variability, and if they are not accounted for in the mathematical model, for example by taking log-ratios or including spot-e ects, then the model will perform poorly. The rst result is reinforced by a simulation study. Practical recommendations are given on how simple loop designs can be extended to more realistic experimental designs and how standard statistical methods allow the experimentalist to use and interpret the results from loop designs in practice.
Appears in Collections:Dept of Mathematics Research Papers

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