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Abstract
Microarray technology is widely applied to address complex scientific questions. However, there remain fundamental issues on how to design experiments to ensure that the resulting data enables robust statistical analysis. Interwoven loop design has several advantages over other designs. However it suffers in the complexity of design. We have implemented an online web application which allows users to find optimal loop designs for two-color microarray experiments. Given a number of conditions (such as treatments or time points) and replicates, the application will find the best possible design of the experiment and output experimental parameters. It is freely available from .
Highlights
Microarray technology is widely used to address complex scientific questions and for studies of gene interactions
The high cost of microarrays plus the complex logistical issues associated with microarray studies, often require that compromises must be made in the number of samples analyzed
Experimental units are at the top layer of the experiment, two RNA samples obtained from each unit are in the middle layer
Summary
To date there is no available tool for biologists to automatically design and visualize the interwoven loop for a microarray experiment Development of such a tool will permit biologist to quickly generate different array hybridization loops, compare the cost and experiment design and efficiently design microarray studies so that robust statistical conclusion can be made. The main point is to generate an optimal number of arrays based on combination of conditions and replicates for two-dye microarray experiment. Pared to 40 required arrays in the optimal loop design in this experiment
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