Following is a scientist's responses to the question, "What's your top advice for designing a microarray analysis experiment to ensure that your statistical analysis, control for error, and normalization procedures will give you an accurate end answer?"
For a complete list of scientists' responses, read the November/December issue of Genome Technology , a GenomeWeb News sister publication.
"My number one piece of advice is to be absolutely sure that all samples are prepared using the same method. If a subset of samples are limiting, then do all samples using the protocol for the most limiting method. Each sample preparation method has an inherent rate of reproducibility, but it will also have an inherent bias. This bias is typically consistent for all samples prepared by that method. If you use two different methods you will be adding a new, uncontrolled factor to your study which will likely make it more difficult to analyze your results.
"My second piece of advice is don't limit yourself on the number of experimental replicates. You will get better data doing one 6x6 comparison than by doing 3x3x3x3. Let the power of your study work for you."
Director, Genomics Core Laboratory
Gladstone Institute of Cardiovascular Disease
University of California, San Francisco