Evaluation of the gene-specific dye bias in cDNA microarray experiments
Evaluation of the gene-specific dye bias in cDNA microarray experiments
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DOI：
10.1093/bioinformatics/bti302
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发表时间：
2005-05-01
期刊：
影响因子：
5.8
通讯作者：
Daudin, JJ
中科院分区：
文献类型：
--
作者：
Martin-Magniette, ML;Aubert, J;Daudin, JJ
动机：在基因芯片实验中，所有样本都被标记为Cy3或Cy5。在双色实验中观察到了系统的和特定于基因的染料偏置效应。与可以通过归一化方法校正的系统效应相比，基因特异性染料偏差并未完全被抑制，并且可能改变关于差异表达基因的结论。方法：使用方差分析模型来考虑基因特异性染料偏差。我们提出了一个指标，称为标记偏向指数，以衡量基因特定的染料偏向。结果：经过低归一化后，我们发现基因特异性染料偏倚是重复序列间实验变异的主要来源。其比值(R/G)可大于2。因此，在没有染料交换的情况下，直接比对可能会发现假阳性基因。讨论了这种伪影的稳定性及其对基因变异和直接或间接比较的影响。
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.Methods: The gene-specific dye bias is taken into account using an analysis of variance model. We propose an index, named label bias index, to measure the gene-specific dye bias. It requires at least two self-self hybridization cDNA microarrays.Results: After lowess normalization we have found that the gene-specific dye bias is the major source of experimental variability between replicates. The ratio (R/G) may exceed 2. As a consequence false positive genes may be found in direct comparison without dye-swap. The stability of this artifact and its consequences on gene variance and on direct or indirect comparisons are addressed.