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Activity Number:
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114
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Type:
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Contributed
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Date/Time:
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Monday, August 9, 2004 : 10:30 AM to 12:20 PM
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Sponsor:
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ENAR
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| Abstract - #301804 |
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Title:
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Effects of Pooling RNA in Microarray Class Comparisons
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Author(s):
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Joanna H. Shih*+ and Aleksandra M. Michalowska and Kevin K. Dobbin and Yumei Ye and Tinghu Qiu
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Companies:
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National Cancer Institute and National Cancer Institute and National Cancer Institute and National Cancer Institute and National Cancer Institute
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Address:
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6130 Executive Blvd., EPN, Room 8132, Bethesda, MD, 20852-7434,
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Keywords:
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microarray ; pooling ; variation ; sample size ; power
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Abstract:
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In microarray experiments investigators sometimes wish to pool RNA samples before labeling and hybridization due to insufficient RNA from each individual sample or to reduce the number of arrays for the purpose of saving cost. The basic assumption of pooling is that the expression of an mRNA molecule in the pool is close to the average expression from individual samples. Recently, a method for studying the effect of pooling mRNA on statistical power in detecting differentially expressed genes between classes has been proposed, but the different sources of variation arising in microarray experiments were not distinguished. We study the implication of pooling in detecting differential gene expression taking into account different sources of variation. We present a formula for the required number of subjects and arrays to achieve the same power as in a nonpooled experiment. We show that due to the loss of degrees of freedom for a pooled design, a large increase of the number of subjects may be required to achieve a comparable power. We also check the adequacy of the model assumption of pooling using real data.
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