Please use this identifier to cite or link to this item: http://buratest.brunel.ac.uk/handle/2438/856
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
Bucca, G
de Jesus, O
Rasaiyaah, J
Smith, CP
Kellam, P
Wit, E
Issue Date: 2004
Publisher: Oxford University Press
Citation: Oxford Journals Life Sciences Bioinformatics 21(4): 492-501
Abstract: Motivation: Despite theoretical arguments that socalled "loop designs" of two-channel DNA microarray experiments are more efficient, biologists keep on using "reference designs". We describe two sets of microarray experiments with RNA from two different 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 efficiency. 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-effects, then the model will perform poorly. The first 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.
URI: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/21/4/492
http://bura.brunel.ac.uk/handle/2438/856
Appears in Collections:Electronic and Computer Engineering
Dept of Mathematics Research Papers
Mathematical Sciences

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