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Bioinformatics Advance Access originally published online on February 2, 2005
Bioinformatics 2005 21(9):1995-2000; doi:10.1093/bioinformatics/bti302
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Published by Oxford University Press 2005.

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

Marie-Laure Martin-Magniette 1,2,*, Julie Aubert 2, Eric Cabannes 3 and Jean-Jacques Daudin 2

1URGV UMR INRA 1165—CNRS 8114—UEVE 2 rue Gaston Crémieux, CP 5708, 91057 Evry Cedex, France
2UMR INAPG/ENGREF/INRA MIA 518 16 rue C. Bernard, 75231 Paris Cedex 05, France
3Laboratoire d'Immunologie Virale, Institut Pasteur 28 rue du Docteur Roux, 75724 Paris, France

*To whom correspondence should be addressed.

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{at}inapg.fr


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