Evaluation of the gene-specific dye bias in cDNA microarray experiments
نویسندگان
چکیده
منابع مشابه
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...
متن کاملEvaluation 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 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 کاملAnswer to the comments of K. Dobbin, J. Shih and R. Simon on the paper 'Evaluation of the gene-specific dye-bias in cDNA microarray experiments'
We would like to thank K. Dobbin, J. Shih and R. Simon for their comments about Martin-Magniette et al. (2005). Their remarks relate to the design of microarray experiments and notably about the use of dye-swaps. We, however, want to make it clear that our manuscript primarily focuses on the detection, quantification and correction of the gene-specific dye-bias introduced in dual-color microarr...
متن کاملAnswer to the comments of K . Dobbin , J . Shih and R . Simon on the paper ‘ Evaluation of the gene - specific dye - bias in cDNA microarray experiments
We would like to thank K. Dobbin, J. Shih and R. Simon for their comments about Martin-Magniette et al. (2005). Their remarks relate to the design of microarray experiments and notably about the use of dye-swaps. We, however, want to make it clear that our manuscript primarily focuses on the detection, quantification and correction of the gene-specific dye-bias introduced in dual-color microarr...
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ژورنال
عنوان ژورنال: Bioinformatics
سال: 2005
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/bti302