Journal Article

Robustness considerations in selecting efficient two-color microarray designs

A. H. M. Mahbub Latif, Frank Bretz and Edgar Brunner

in Bioinformatics

Volume 25, issue 18, pages 2355-2361
Published in print September 2009 | ISSN: 1367-4803
Published online July 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp407
Robustness considerations in selecting efficient two-color microarray designs

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The main goal of microarray experiments is to select a small subset of genes that are differentially expressed among competing mRNA samples. For a given set of such mRNA samples, it is possible to consider a number of two-color cDNA microarray designs with a fixed number of arrays. Appropriate criteria can be used to select an efficient design from such a set of alternative experimental designs. In practice, however, microarray expression data often contain missing observations and the most efficient design (with complete observations) for a specific setup may not be efficient in the presence of missing observations. In this article, we propose two criteria to address the robustness of microarray designs against missing observations. We demonstrate the simultaneous use of efficiency and robustness criteria to select good microarray designs for both one-factor and multi-factor experiments.

Contact: mlatif@isrt.ac.bd

Journal Article.  5798 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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