Experimental designs for 2-colour cDNA microarray experiments

✍ Scribed by Nam-Ky Nguyen; E. R. Williams

• Publisher: John Wiley and Sons
• Year: 2006
• Tongue: English
• Weight: 233 KB
• Volume: 22
• Category: Article
• ISSN: 1524-1904
• DOI: 10.1002/asmb.654

✦ Synopsis

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 $ \left(v \atop 2 \right)$. 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. Copyright © 2006 John Wiley & Sons, Ltd.