Microarray technology allows the monitoring of mRNA levels in cells for thousands of genes simultaneously. Linear mixed models are generally used to assess significance of differential expression among treatments. In this paper we estimate the effect of recovering intra slide information in two variants of reference designs. Treating arrays as random effects allows the recovery of inter array information and yields more precise estimates of the treatment difference than the fixed array specification. The comparison of designs may also be affected by the recovery of inter-array information. Analytical or numerical analysis of the recovery of inter array information is readily available using mixed model theory.
Proceedings of the World Congress on Genetics Applied to Livestock Production, Volume , , 23.23, 2006
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