Algorithmic construction of optimal block designs for two-colour cDNA microarray experiments using the linear mixed effects model |
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Authors: | Legesse K Debusho Dibaba B Gemechu Linda M Haines |
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Institution: | 1. Department of Statistics, University of South Africa, Science Campus, Florida, South Africadebuslk@unisa.ac.za;3. Department of Statistics, University of South Africa, Science Campus, Florida, South Africa;4. Department of Statistical Sciences, University of Cape Town, Rondebosch, South Africa |
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Abstract: | ABSTRACTIn this study, methods for efficient construction of A-, MV-, D- and E-optimal or near-optimal block designs for two-colour cDNA microarray experiments with array as the block effect are considered. Two algorithms, namely the array exchange and treatment exchange algorithms together with the complete enumeration technique are introduced. For large numbers of arrays or treatments or both, the complete enumeration method is highly computer intensive. The treatment exchange algorithm computes the optimal or near-optimal designs faster than the array exchange algorithm. The two methods however produce optimal or near-optimal designs with the same efficiency under the four optimality criteria. |
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Keywords: | Array exchange algorithm A- MV- D- and E-optimal designs Complete enumeration Microarray experiment Treatment exchange algorithm |
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