Dye bias correction in dual-labeled cDNA microarray gene expression measurements.

Dye bias correction in dual-labeled cDNA microarray gene expression measurements.

A significant limitation to the analytical accuracy and precision of dual-labeled spotted cDNA microarrays is the signal error due to dye bias. Transcript-dependent dye bias may be due to gene-specific differences of incorporation of two distinctly different chemical dyes and the resultant differential hybridization efficiencies of these two chemically different targets for the same probe. Seve...

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

In their paper in Bioinformatics, Martin-Magniette et al. (2005) recommend complete dye-swap1 designs for both direct and indirect dual label microarray experiments. These recommendations contradict our previous recommendations (Dobbin et al., 2003) for designing experiments, where we suggested minimizing or eliminating the use of dye-swap arrays. We show here that the recommendations of Martin...

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

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. M...

cDNA Microarray Data Normalization

Characterizing dye bias in microarray experiments

MOTIVATION Spot intensity serves as a proxy for gene expression in dual-label microarray experiments. Dye bias is defined as an intensity difference between samples labeled with different dyes attributable to the dyes instead of the gene expression in the samples. Dye bias that is not removed by array normalization can introduce bias into comparisons between samples of interest. But if the bias...