Following are scientists' 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.
"Most researchers use reference designs when doing two-color cDNA microarray experiments and only print one spot per gene. My advice to researchers using two-color arrays is to print the slides with several replicate spots per slide to provide insurance against bad spots and improve the control of error at low cost. Secondly, to use balanced, incomplete block designs (i.e. loop designs) whenever possible to reduce the cost and increase the accuracy of the results for the same number of slides. Finally, discuss the experiment with a statistician to insure that the true replication of the experiment is being done at the level of the independent biological samples."
James L Rosenberger
Department of Statistics
Penn State University