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


BACKGROUND
http://www.inapg.inra.fr/ens_rech/mathinfo/recherche/mathematique
Martin-Magniette
Marie-Laure
ML
URGV UMR INRA 1165--CNRS 8114--UEVE, Evry, France. mlmartin@inapg.fr
Aubert
Julie
J
Cabannes
Eric
E
Daudin
Jean-Jacques
JJ
D000465:Algorithms; D016477:Artifacts; D005456:Fluorescent Dyes; D020869:Gene Expression Profiling / Q000379:methods*; D017404:In Situ Hybridization, Fluorescence / Q000379:methods*; D008957:Models, Genetic; D015233:Models, Statistical; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D011786:Quality Control; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity
D005456:Fluorescent Dyes