© 2003 by Oxford University Press
© 2003 Oxford University Press
COMMENTARY |
Questions and Answers on Design of Dual-Label Microarrays for Identifying Differentially Expressed Genes
Affiliation of authors: Biometric Research Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD.
Correspondence to: Kevin Dobbin, PhD, National Cancer Institute, 6130 Executive Blvd., EPN 8124, Bethesda, MD 20892–7434 (e-mail: dobbinke@mail.nih.gov).
| The first 150 words of the full text of this article appear below. |
The rapid growth in the use of microarrays has generated many questions about how to design experiments that use this technology effectively. Investigators need answers to questions about RNA sample selection, allocation of samples to arrays, robustness of design, dye bias, sample size, and statistical power to ensure that the experimental objectives are achieved. We address some common questions that arise in designing dual-label microarray experiments and provide statistical answers to these questions, focusing specifically on how to select optimal designs for the identification of differentially expressed genes.
BACKGROUND
The dual-label microarray measures the expression level of thousands of genes for a sample of cells. A common goal of microarray experiments is to determine which genes are differentially expressed among two or more predefined classes of biologic specimens. These types of study goals are referred to as "class comparisons" (1). Some examples of class comparisons are 1) identifying
SAMPLE SELECTION
Is It Sufficient to Sample One Individual From Each Class?
How Many Replicates of Each RNA Sample Should Be Hybridized?
What Are the Advantages and Disadvantages of Pooling Samples?
PAIRING SAMPLES FOR CO-HYBRIDIZATION
What Types of Designs Should Be Considered?
Which Design Will Provide the Best Class Comparisons?
What Happens If the Class Definitions Change?
What If We Also Plan to Perform Class Discovery on the Samples?
What Is Sacrificed If a Reference Design Is Not Used?
DYE BIAS
What Is the Source of Dye Bias?
Does Gene-Specific Dye Bias Exist?
When Is Gene-Specific Dye Bias an Issue?
How Should I Design an Experiment to Eliminate Dye Bias From the Class Comparisons?
How Will Class Discovery Results Be Affected by Dye Bias?
How Can Dye Bias Be Eliminated From Comparisons Between the Reference and the Nonreference Samples in a Reference Design?
SAMPLE SIZE
How Many Biologic Samples Are Needed for a Reference Design?
What Sample Size Should Be Used for a Balanced Block Design?
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