Design issues for cDNA microarray experiments

Microarray experiments are used to quantify and compare gene expression on a large scale. As with all large- scale experiments, they can be costly in terms of equipment, consumables and time. Therefore, careful design is particularly important if the resulting experiment is to be maximally informative, given the effort and the resources. What then are the issues that need to be addressed when planning microarray experiments? Which features of an experiment have the most impact on the accuracy and precision of the resulting measurements? How do we balance the different components of experimental design to reach a decision? For example, should we replicate, and if so, how?