Near-optimal designs for dual-channel microarray studies
by Ernst Wit, Agostino Nobile and Raya Khanin
Much biological and medical research employs microarray studies to monitor
gene expression levels across a wide range of organisms and under many
experimental conditions.
Dual channel microarrays are a common platform and allow two samples to be
measured simultaneously.
A frequently used design uses a common reference sample to make conditions
across different arrays comparable. Our aim is to formulate microarray
experiments in the experimental design context and to use simulated annealing
to search for near-optimal designs.
We identify a subclass of designs, the so-called interwoven loop designs,
that seems to have good optimality properties compared with the near-optimal
designs that are found by simulated annealing. Commonly used reference
designs and dye swap designs are shown to be highly inefficient.
Keywords:
Loop designs; Microarray experiments; Optimal design; Simulated annealing