Validation of Toxicogenomic Technologies A Workshop Summary (2007) / Chapter Skim
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Attachment 1. Experimental Objectives of DNA Microarray Studies
Attachment 1. Experimental Objectives of DNA Microarray Studies
Pages 39-48
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Three common types of objectives in microarray studies are class comparison, class prediction and class discovery. In class comparison studies, the goal is to identify genes differentially expressed among predefined classes of samples.
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Technical replicates occur when the same sample is measured multiple times. For example, one may pipette out multiple RNA samples from the same test tube and run each on a different array.
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If, for example, one only has one sample from each of two classes, then one cannot assess the statistical significance of observed fold changes without knowing whether these are outside the range of the normal biologic variations observed in the populations. In general, the higher the level of replication the better, so that biologic replicates are preferable to technical replicates.
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A relative efficiency of 2.4 means that 2.4 times as many arrays are required for a reference design to equal the accuracy of a balanced block design. This is the relative efficiency for two classes, and it depends on the ratio of technical to biologic variation (Dobbin and Simon 2002)
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For example, "A1" indicates biologic sample 1 from class A "R" indicates the reference sample, which is subsampled multiple times.
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46 Validation of Toxicogenomic Technologies block design may make some of these alternative comparisons impossible or inefficient. Another potential drawback is that data from different block design experiments cannot be effectively combined together, whereas if the same reference sample is used the data from different experiments can be combined for analysis.
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2005. Sample size determination in microarray experiments for class comparison and prognostic classification.
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2005. Charac terizing dye bias in microarray experiments.
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