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Experiments on all three platforms were done using a reference design approach.
Array hybridizations were performed using a reference design.
Array hybridizations were performed using a reference design, where each sample was compared to a common reference sample.
Experiments were performed on this platform using a reference design as indicated by Knapen et al. [ 32].
Data sets B-D were generated from paired samples using a reference design on cDNA arrays; Paired t-tests are appropriate for these three data sets.
Total RNA is collected at three post-treatment time points and compared, using a reference design, to RNA extracted from untreated plants.
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As described in the Methods section, we used a reference design to collect the data.
However, the contribution of increased number of stages studied to the overall number of significantly regulated genes was greatly mitigated by the fact that we used a reference design in which each life-cycle stage was compared to a mixture of all four life-cycle stages.
In theory, using a reference sample design instead of a direct comparison design should increase the variance by a factor of 2. This increase has in fact been observed in practice [ 33].
The second part of the thesis focuses on reverse engineering where we present two algorithms to infer high-level blocks in an untrusted circuit by using a reference behavioral design or a corresponding block diagram accompanied by a natural-language document.
Gene expression changes were catalogued within each group using a reference hybridization design and a targeted immunospecific cDNA microarray platform (BOTL-5) with 4,800 spot features representing 1,391 genes.
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