寡聚核苷酸芯片表达谱系统偏移的校正算法
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国家自然科学基金资助项目(60471003)


A Robust Method to Normalize System Bias for High-density Oligonucleotide Array Gene Expression Profile
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This work was supported by a grant from The National Natural Science Foundation of China(60471003)

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    摘要:

    多芯片对比实验中,由于多方面的变异因素,使得芯片间存在明显的系统偏移. 因此,芯片表达谱数据的校正处理是关键的数据预处理步骤. 当前,已经提出了很多校正算法,比如:比例常数校正、非线性校正、分位数校正等. 提出了一种新的校正算法. 在选择的最小秩差异探针集上,进行非线性M-A校正. 并采用迭代策略减弱基准芯片方法对基准芯片选择的敏感性. 在标准测试集上,同几种已知的方法进行了对比分析.

    Abstract:

    In multiarray experiments, there is some system bias, which contaminated by experimental factors such as spot location (often referred to as a print-tip effect), arrays, dyes, and various interactions of these effects. For comparable each other, it is necessary to normalize the raw expression profile data. Normalization is the key step in low level processing. In fact, many normalization methods have been developed, i.e. Scaling normalization, Nonlinear normalization, Quantile normalization and so on. New baseline normalization is presented. First, select the subset of probes, which have the min rank range. Second, do nonlinear normalization on robust baseline. Iterative strategy weakens the sensitivity of the baseline method to select baseline. With the standard test dataset, compare it with other methods. The results show that the novel method has better performances than others in several ways.

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邱浪波,王广云,王正志.寡聚核苷酸芯片表达谱系统偏移的校正算法[J].生物化学与生物物理进展,2006,33(6):556-561

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历史
  • 收稿日期:2005-12-09
  • 最后修改日期:2006-03-20
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  • 在线发布日期: 2006-06-14
  • 出版日期: 2006-06-20