Development of a generic microarray analysis platform using BASE and Limma

Using BASE (BioArray Software Environment) and some of the R-packages bundled in Bioconductor, we are developing a generic platform for microarray data analysis in close collaboration with the Intelligent Systems Laboratory (University of Antwerp).

Starting from the very beginning of the microarray analysis workflow, research has gone into advantages and disadvantages of different hybridisation design strategies (control versus exposed, universal reference, interwoven loop, A-optimal design, ...), and the implications of experimental setup on the microarray hybridisation design.

Further, we are testing and building an algorithm for microarray data analysis, choosing different analysis steps (background correction, normalisation, duplicate correlation, contrast definition, ...) based on literature and own experiments. Our approach offers flexibility and control in terms of hybridisation design support, support for both technical and biological replication, custom contrast definition and user controllable analysis parameters.