Sankhya: The Indian Journal of Statistics

2002, Volume 64, Series A, Pt. 3, 707--721

DIRECT VERSUS INDIRECT DESIGNS FOR cDNA MICROARRAY EXPERIMENTS

By

TERENCE P. SPEED, University of California, Berkeley, USA and The Walter and Eliza Hall Institute, Australia
and
YEE HWA YANG, University of California, San Francisco

SUMMARY. We calculate the variances of two classes of estimates of differential gene expression based on log-ratios of fluorescence intensities from cDNA microarray experiments: direct estimates, using measurements from the same slide, and indirect estimates, using measurements from different slides. These variances are compared and numerical estimates are obtained from a small experiment involving 4 slides. Some qualitative and quantitative conclusions are drawn which have potential relevance to the design of cDNA microarray experiments.

AMS (1991) subject classification}. Primary 92B15; secondary 62H99, 62J10.

Key words and phrases. cDNA microarray analysis; differential gene expression; experimental design; common reference design; technical replicates.

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