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Some examples of nicely done microarray studies

• Caldo, Nettleton and Wise (2004) Plant Cell
• Jin et al (2001) Nature Genetics

General Principles of Experimental Design (Textbooks)

• Montgomery (2005) Design and Analysis of Experiments
• Kuehl (2000) Design of Experiments: Statistical Principles of Research Design and Analysis

Comparisons of Measurement Platforms

• Cao et al (2003) Alliance for Cellular Signaling
• Irizarry et al (2004) Berkeley Electronic Press
• Marioni et al (2008) Genome Research
• Bullard et al (2009) BMC Bioinformatics

Sample size

• Black and Doerge (2002) Bioinformatics
• Cui and Churchill (2003) Methods of microarray data analysis
• Gadbury et al (2004) Statistical Methods in Medical Research

Sample pooling

• Kendziorski, Zhang and Attie (2003) Biostatistics

Sample Amplification

• L. Petalidis et al (2003) Nucleic Acid Research

Experiment Design for 2-channel Arrays

• Altman and Hua (2006) Genetical Research
• Kerr (2003) Biometrics
• Yang and Speed (2002) Nature Reviews: Genetics

Experiment Design for Sequencing Data

• Fang and Cui (2010) Briefings in Bioinformatics
• Auer and Doerge (2010) Genetics
• Nettleton (2014) book chapter