Near-optimal designs for dual channel microarray studies

Wit, E., Nobile, A. and Khanin, R. (2005) Near-optimal designs for dual channel microarray studies. Journal of the Royal Statistical Society: Series C (Applied Statistics), 54(5), pp. 817-830. (doi: 10.1111/j.1467-9876.2005.00519.x)

Abstract

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.

• Item Type: Articles
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Nobile, Dr Agostino and Khanin, Dr Raya
• Authors: Wit, E., Nobile, A., and Khanin, R.
• College/School: College of Science and Engineering > School of Mathematics and Statistics > Statistics
• Journal Name: Journal of the Royal Statistical Society: Series C (Applied Statistics)
• ISSN: 0035-9254
• Published Online: 01 July 2005