Design of microarray experiments
Dr Penny Sanchez with G Glonek and A Metcalfe
Microarrays are a powerful technology that enables the measurement of the expression levels of many thousands of genes simultaneously. Rigorous statistical design of microarray experiments is critical for realizing the full potential of this technology.
Our methodology is aimed at the recommendation of optimal designs for a diverse range of two-colour microarray experiments. Based on statistical efficiency, the criterion of Pareto optimality is employed to optimise for the effects of particular scientific interest. A design is defined to be Pareto optimal if there is no other design that leads to equal or greater precision for each of the effects of scientific interest and greater precision for at least one such effect.
For elementary experiments, an exhaustive search for Pareto optimal designs can be carried out, as presented in Sanchez and Glonek (2009). However, this is infeasible for larger and more complex experiments.
To cater for situations for which an exhaustive search is infeasible, the methodology we have developed is an adaptation of the multiple objective metaheuristic method of Pareto simulated annealing to the microarray context. Based on a guided search, to explore the design space in an efficient way, our method is carried out to generate near-optimal designs in a relatively short amount of time. This is crucial to enable the recommendation of optimal designs that make the most effective use of resources for complex microarray experiments.
Investigators and affiliations
Dr Penny Sanchez, University of South Australia
Assoc Prof Gary Glonek, University of Adelaide
Assoc Prof Andrew Metcalfe, University of Adelaide
P. S. Sanchez; G. F. V. Glonek, Optimal designs for two-colour microarray experiments, Biostatistics 2009; doi:10.1093/biostatistics/kxp012.
Areas of study and research
- Health Research
- Alliance for Research in Exercise, Nutrition and Activity (ARENA)
- Centre for Cancer Biology
- Centre for Drug Discovery and Development
- Centre for Population Health Research
- Centre of Research Excellence for the Prevention of Chronic Conditions in Rural and Remote High Risk Populations
- International Centre for Allied Health Evidence
- Medicine and Device Surveillance CRE
- Quality Use of Medicines and Pharmacy Research Centre
and Social Sciences
- Art, Architecture and Design
- Communication, International Studies and Languages
- Psychology, Social Work and Social Policy
- Hawke Research Institute
- Asia Pacific Centre for Work Health and Safety
- Australian Centre for Child Protection
- Barbara Hardy Institute
- Centre for Research in Education
- Hawke EU Jean Monnet Centre of Excellence
- Centre for Islamic Thought and Education
- International Centre for Muslim and non-Muslim Understanding
- Research Centre for Languages and Cultures
- Zero Waste SA Research Centre for Sustainable Design and Behaviour (sd+b)
IT, Engineering and
- Future Industries Institute
- UniSA College