Experimental designs for 2-colour cDNA microarray experiments

Abstract

Kerr and Churchill (Biostatistics 2001; 2:183-201) showed how varieties (e.g. type of tissues, drug treatments, etc.) are paired onto arrays by a catalogue of A-optimal incomplete block designs (IBDs) for 6-10 varieties (v), and number of blocks of size 2 between v and (2v). These A-optimal IBDs were obtained by (i) generating all non-isomorphic connected graphs on v vertices using Brendan McKay's, MAKEG program (http://cs.anu.edu.au/ people/bdm/nauty/) and (ii) comparing all designs of the same size on the basis of A-optimality to obtain the best ones. In this paper we will give a quick overview on IBDs and describe an algorithmic approach to extend the mentioned catalogue. We aim at IBDs with up to 100 varieties with equal as well as unequal replications. A catalogue of 2007 IBDs is given. We will also extend the concept of even designs in Kerr and Churchill (Biostatistics 2001; 2:183-201) to row-orthogonal designs. Show more