Optimal Design of Single Factor cDNA Microarray experiments and Mixed Models for Gene Expression Data
Microarray experiments are used to perform gene expression profiling on a large scale. E- and A-optimality of mixed designs was established for experiments with up to 26 different varieties and with the restriction that the number of arrays available is equal to the number of varieties. Because the...
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Virginia Tech
2014
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Online Access: | http://hdl.handle.net/10919/26379 http://scholar.lib.vt.edu/theses/available/etd-03072003-100835/ |
Summary: | Microarray experiments are used to perform gene expression profiling on a large scale. E- and
A-optimality of mixed designs was established for experiments with up to 26 different varieties
and with the restriction that the number of arrays available is equal to the number of
varieties. Because the IBD setting only allows for a single blocking factor (arrays), the search
for optimal designs was extended to the Row-Column Design (RCD) setting with blocking
factors dye (row) and array (column). Relative efficiencies of these designs were further compared under analysis of variance (ANOVA) models. We also compared the performance of
classification analysis for the interwoven loop and the replicated reference designs under four
scenarios. The replicated reference design was favored when gene-specific sample variation
was large, but the interwoven loop design was preferred for large variation among biological
replicates.
We applied mixed model methodology to detection and estimation of gene differential expression.
For identification of differential gene expression, we favor contrasts which include
both variety main effects and variety by gene interactions. In terms of t-statistics for these
contrasts, we examined the equivalence between the one- and two-step analyses under both
fixed and mixed effects models. We analytically established conditions for equivalence under
fixed and mixed models. We investigated the difference of approximation with the two-step
analysis in situations where equivalence does not hold. The significant difference between
the one- and two-step mixed effects model was further illustrated through Monte Carlo simulation
and three case studies. We implemented the one-step analysis for mixed models with
the ASREML software. === Ph. D. |
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