In this article we propose two practical types of designs for large time-course, dual-channel microarray experiments. One type consists of several interwoven loops, and the other type combines reference and loop designs. By representing the experiment as a graph, where the timepoints are nodes and the arrays are edges, we demonstrate how the time contrasts between any two timepoints can be estimated, provided that there is a path of edges linking them. In addition, we give a general formula for the variance of such contrasts. The efficiency of the proposed designs is evaluated by estimating the variances of the log-ratios of the comparisons of interest.
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Churchill GA. Fundamentals of experimental design for cDNA microarrays. Nat Genet 2002; 32 Suppl.: 490–5
Kerr MK, Churchill GA. Statistical design and the analysis of gene expression microarray data. Genet Res 2001; 77: 123–8
Dobbin K, Shih JH, Simon R. Statistical design of reverse dye microarrays. Bioinformatics 2003; 19(7): 803–10
Yang YH, Speed T. Design issues for cDNA microarray experiments. Nat Rev Genet 2002; 3: 579–88
Kendziorski CM, Zhang Y, Lan H, et al. The efficiency of mRNA pooling in microarray experiments. Biostatistics 2003; 4(3): 465–77
Kerr M, Churchill GA. Experimental design for gene expression microarrays. Biostatistics 2001; 2: 183–201
Glonek GFV, Solomon PJ. Factorial and time course designs for cDNA microarray experiments. Biostatistics 2004; 5(1): 89–111
Black MA, Doerge RW. Calculation of the minimum number of replicate spots required for detection of significant gene expression fold change in microarray experiments. Bioinformatics 2002; 18(12): 1609–16
Landgrebe J, Bretz F, Brunner E. Efficient design and analysis of two colour factorial microarray experiments. Comput Stat Data Anal 2006; 50(2): 499–51
Lee ML, Kuo FC, Whitmore GA, et al. Importance of replication in microarray gene expression studies: statistical methods and evidence from repetitive cDNA hybridizations. Proc Natl Acad Sci USA 2000; 97(18): 9834–9
Tjur T. Block designs and electrical networks. Ann Stat 1991; 19(2): 1010–27
Jin W, Riley RM, Wolfinger RD, et al. The contribution of sex, genotype and age to transcriptional variance in Drosophila melanogaster. Nat Genet 2001; 29: 389–95
Vinciotti V, Khanin R, D’Alimonte D, et al. An experimental evaluation of a loop versus a reference design for two-channel microarrays. Bioinformatics 2005 Feb 15; 21(4): 492–501
Churchill GA, Oliver B. Sex, flies and microarrays. Nat Genet 2001; 29: 355–6
Wit E, Nobile A, Khanin R. Near-optimal designs for dual-channel microarray studies. J R Stat Soc Ser C Appl Stat 2005; 54(5): 817–30
The authors are grateful to Agostino Nobile (University of Glasgow) for the suggestion to consider a carriage wheel design, for interesting discussions on the subject of design of microarray experiments and for valuable comments on this paper.
This research has been funded by the Biotechnology and Biological Sciences Research Council (BBSRC), UK, programme ‘Exploiting Genomics’.
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Khanin, R., Wit, E. Design of Large Time-Course Microarray Experiments with Two Channels. Appl-Bioinformatics 4, 253–261 (2005). https://doi.org/10.2165/00822942-200504040-00005
- Outer Loop
- Distant Point
- Efficient Design
- Loop Design
- Consecutive Point