Gene-specific dye bias in microarray reference designs
نویسندگان
چکیده
منابع مشابه
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...
متن کاملComment 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...
متن کاملCharacterizing 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...
متن کاملDye 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...
متن کاملCorrecting for gene-specific dye bias in DNA microarrays using the method of maximum likelihood
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 magni...
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ژورنال
عنوان ژورنال: FEBS Letters
سال: 2004
ISSN: 0014-5793
DOI: 10.1016/s0014-5793(04)00083-3