Experimental designs for 2-colour cDNA microarray experiments

Nam Ky Nguyen; E. R. Williams

doi:10.1002/asmb.654

Experimental designs for 2-colour cDNA microarray experiments

Nam Ky Nguyen, E. R. Williams^*

^*Corresponding author for this work

The Australian National University

Research output: Contribution to journal › Article › peer-review

7 Citations (Scopus)

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 (₂^v). 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.

Original language	English
Pages (from-to)	631-638
Number of pages	8
Journal	Applied Stochastic Models in Business and Industry
Volume	22
Issue number	5-6
DOIs	https://doi.org/10.1002/asmb.654
Publication status	Published - Sept 2006

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title = "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.",

keywords = "A-optimality, Even designs, Incomplete block designs, Optimal designs, Row-column designs, Row-orthogonal designs",

author = "Nguyen, {Nam Ky} and Williams, {E. R.}",

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AU - Williams, E. R.

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N2 - 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.

AB - 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.

KW - A-optimality

KW - Even designs

KW - Incomplete block designs

KW - Optimal designs

KW - Row-column designs

KW - Row-orthogonal designs

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JO - Applied Stochastic Models in Business and Industry

JF - Applied Stochastic Models in Business and Industry

IS - 5-6

ER -

Experimental designs for 2-colour cDNA microarray experiments

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