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.
A. I'd like to emphasize a few key points special for two-color microarray
1) Confirm informatics of the array design and layout to be correct.
2) Use as few treatment conditions as possible.
3) Sample RNA from separate biological resources for a replicated microarray experiment.
4) Use high-quality RNA.
5) Use a common reference RNA for each hybridization.
6) Use equal length of cDNA for Cy3- and Cy5-labeled probes.
7) Use equal amount of dye concentrations for the labeled probes.
8) Use exogenous nucleic acid (external RNA) as spiking-in controls.
9) Use the control genes as a reference for the first step of normalization and estimate CV for the microarray.
Z. Lewis Liu
Research Molecular Biologist