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Bioinformatics Advance Access published online on February 2, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti302
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Bioinformatics © Oxford University Press 2005; all rights reserved.
Received July 7, 2004
Revised January 25, 2005
Accepted January 27, 2005

Article

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

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

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

* To whom correspondence should be addressed.
Marie-Laure Martin-Magniette, E-mail: mlmartin{at}inapg.fr


  Abstract

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 (LBI), 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 artefact 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.


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