Evaluation of the gene-specific dye bias in cDNA microarray experiments

• Published in: Bioinformatics Vol. 21; no. 9; pp. 1995 - 2000
• Main Authors: Martin-Magniette, Marie-Laure, Aubert, Julie, Cabannes, Eric, Daudin, Jean-Jacques
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 01.05.2005; Oxford Publishing Limited (England)
• Subjects: Algorithms; Biological and medical sciences; Fluorescent Dyes; Fundamental and applied biological sciences. Psychology; Gene Expression Profiling - methods; General aspects; In Situ Hybridization, Fluorescence - methods; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Models, Genetic; Models, Statistical; Oligonucleotide Array Sequence Analysis - methods; Quality Control; Reproducibility of Results; Sensitivity and Specificity; Variance analysis; Evaluation; Dyes; Gene; Sample; Bias; Color; DNA chip; Method
• ISSN: 1367-4803; 0266-7061; 1460-2059; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/bti302

Motivation: In cDNA microarray experiments all samples are labeled with either Cy3 or Cy5. Systematic and gene-specific dye bias effects have been observed in dual-color experiments. In contrast to systematic effects which can be corrected by a normalization method, the gene-specific dye bias is not completely suppressed and may alter the conclusions about the differentially expressed genes. Methods: The gene-specific dye bias is taken into account using an analysis of variance model. We propose an index, named label bias index, to measure the gene-specific dye bias. It requires at least two self–self hybridization cDNA microarrays. Results: After lowess normalization we have found that the gene-specific dye bias is the major source of experimental variability between replicates. The ratio (R/G) may exceed 2. As a consequence false positive genes may be found in direct comparison without dye-swap. The stability of this artifact and its consequences on gene variance and on direct or indirect comparisons are addressed. Availability: http://www.inapg.inra.fr/ens_rech/mathinfo/recherche/mathematique Contact: mlmartin@inapg.fr