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Ann N Y Acad Sci. 2004 May;1020:110-23.

Numerical deconvolution of cDNA microarray signal: simulation study.

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  • 1Biometry Research Group, Division of Cancer Prevention, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, EPN 3136, 6130 Executive Boulevard, Rockville, MD 20892, USA.


A computational model for simulation of the cDNA microarray experiments has been created. The simulation allows one to foresee the statistical properties of replicated experiments without actually performing them. We introduce a new concept, the so-called bio-weight, which allows for reconciliation between conflicting meanings of biological and statistical significance in microarray experiments. It is shown that, for a small sample size, the bio-weight is a more powerful criterion of the presence of a signal in microarray data as compared to the standard approach based on t test. Joint simulation of microarray and quantitative PCR data shows that the genes recovered by using the bio-weight have better chances to be confirmed by PCR than those obtained by the t test technique. We also employ extreme value considerations to derive plausible cutoff levels for hypothesis testing.

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