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

M.-L. Martin-Magniette, J. Aubert, E. Cabannes, J.-J. Daudin
2005 Bioinformatics  
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
more » ... 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 genespecific 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.
doi:10.1093/bioinformatics/bti302 pmid:15691855 fatcat:urbppi65jjftrbuzscw2eeiwwy