Microarray experiments experimental designs

Eor every microarray experiment the first and most important step is experimental design. A badly designed experiment can render microarray data unsuitable for addressing the experimental questions or worse, lead the investigator to draw false conclusions. Furthermore, failed microarray experiments can be very costly both in terms of resources and time. There are many issues that must be addressed when planning a cDNA microarray experiment, some intuitive, others requiring considerable thought. 

Simon R. Dobbin K. 2003. Experimental design of DNA microarray experiments. Bio Techniques 34 S16. 

In Sections 2 to 4, we review the technology of synthetic oligonucleotide microarrays and describe some of the popular statistical methods that are used to discover genes with differential expression in simple comparative experiments. A novel Bayesian procedure is introduced in Section 5 to analyze differential expression that addresses some of the limitations of current procedures. We proceed, in Section 6, by discussing the issue of sample size and describe two approaches to sample size determination in screening experiments with microarrays. The first approach is based on the concept of reproducibility, and the second approach uses a Bayesian decision-theoretic criterion to trade off information gain and experimental costs. We conclude, in Section 7, with a discussion of some of the open problems in the design and analysis of microarray experiments that need further research. 

Jane Chang is an Assistant Professor in the Department of Applied Statistics and Operations Research at Bowling Green State University. Her research interests are in optimal experimental design, the design and analysis of microarray experiments, and multiple testing in two-level factorial designs. 

Figure 3.3. Schematic of a microarray experiment. (A) Experimental design incorporating both biological and technical replication. There are three treated mice and three control mice, providing biological replication. RNA from each mouse is labeled with each dye and hybridized more than once, providing technical replication. The hybridization design uses a loop design as shown in Figure 3.2. (B) Outline of the wet and dry lab steps involved in a microarray experiment. See color insert.

A microarray experiment, as any other experiment, starts with an experimental design where the allocation of samples to experimental conditions, the sample size, and all the usual important aspects of an experiment are performed (36,43). In the following paragraph one can assume that this has been done for some experimental conditions and that one or two samples are available to be hybridized on two- or one-color microarrays. This is done following the steps described below and outlined in Figure 8. 

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