Following are scientist responses to the question, "What'syour 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 theNovember/December issue of Genome Technology, a GenomeWeb News sister publication.
"To be very honest, a large proportion of array experiments in the past were of very poor quality and no amount of clever statistical manipulation would give you good results (the garbage in = garbage out principle). The array companies are putting out very good slides and our 'roll your own' are much more reliable now because of better printing instruments, substrates (slides), etc. I am going to enclose a couple of papers by Richard Simon at the NCI who is the expert in the questions you have asked: Journal of the National Cancer Institute, Vol. 95, No. 18, September 17, 2003, pp. 1362-1369; and BMC Bioinformatics 2003, 4:33, 02 September 2003. Also available here."
National Cancer Institute, NIH