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Genome Technology s Lab Notebook: Reader Tips and Experiences: Feb 3, 2005

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

NationalCenterfor Agricultural Utilization Research

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