Correcting for gene-specific dye bias </titl> </head> <body> <h1>Correcting for gene-specific dye bias in DNA microarrays using the method of maximum likelihood.</h1> <p> <b>Motivation:</b> 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. </p> <p> <b>Results:</b>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 differentially expressed genes within this framework. Improvement is also possible in related ANOVA approaches. </p> <p> <b>Availability:</b>A software implementation of this procedure in MATLAB is freely available <A href="VERA.tgz">here</A>. </p> <p> <b>Contact:</b> <a href="mailto:rmkelley@ucsd.edu">rmkelley@ucsd.edu</a> </p> </body> </html>