Correcting for gene-specific dye bias in DNA microarrays using the method of maximum likelihood.

ABSTRACT:

Motivation

In two-color microarray experiments, well-known differences exist in the labeling and hybridization efficiency of Cy3 and Cy5 dyes. Previous reports have revealed that these differences can vary on a gene-by-gene basis, an effect termed gene-specific dye bias. If uncorrected, this bias can influence the determination of differentially expressed genes.

Results

We show that the magnitude of the bias scales multiplicatively with signal intensity and is dependent on which nucleotide has been conjugated to the fluorescent dye. A method is proposed to account for gene-specific dye bias within a maximum-likelihood error modeling framework. Using two different labeling schemes, we show that correcting for gene-specific dye bias results in the superior identification of di

SUBMITTER: Kelley R 

PROVIDER: S-EPMC2811084 | biostudies-literature | 2008 Jan

REPOSITORIES: biostudies-literature