Direct versus indirect designs for cDNA microarray experiments

April, 2002
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S.N. Evans, B. Hansen and P.B. Stark

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.

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