A model-based background adjustment for oligonucleotide expression arrays
A model-based background adjustment for oligonucleotide expression arrays
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DOI：
10.1198/016214504000000683
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发表时间：
2004-12-01
影响因子：
3.7
通讯作者：
Spencer, F
中科院分区：
文献类型：
--
作者：
Wu, ZJ;Irizarry, RA;Spencer, F
高密度寡核苷酸表达阵列广泛应用于生物医学研究的许多领域。Affymetrix基因芯片阵列是最流行的，在Affymetrix系统。在图像处理步骤之后，会进行相当数量的进一步预处理和数据缩减。学术团体开发的统计程序在改进Affymetrix系统提供的默认算法方面取得了成功。在本文中，我们提出了一种基于正式统计框架的预处理步骤-背景调整的解决方案。我们的解决方案大大提高了该技术在各种实际应用中的性能。这些阵列使用短的寡核苷酸来探测RNA样本中的基因。通常，每个基因由11-20对寡核苷酸探针表示。这些对的第一个组成部分被称为完美匹配探针，被设计为只与来自预期基因的转录本杂交。特定的杂交)。然而，与其他序列的杂交（即非特异性杂交）是不可避免的。此外。杂化强度由引入光噪声的扫描器测量。因此，观察到的强度需要调整，以提供特定杂交的准确测量。我们发现，默认的临时调整，作为Affymetrix系统的一部分，可以通过使用来自使用探针序列信息的统计模型的估计器来改进。预处理的最后一步是总结每个基因的探针水平数据，以定义代表相应mRNA物种数量的表达度量。在本文中，我们说明了没有适当调整非特异性杂交存在的实际后果，并提供了基于我们的背景调整程序的解决方案。计算我们的调整的软件是生物导体项目（http://bioconductor.org）的一部分。
High-density oligonucleotide expression arrays are widely used in many areas of biomedical research. Affymetrix GeneChip arrays are the most popular, In the Affymetrix system. a fair amount of further preprocessing and data reduction occurs after the image-processing step. Statistical procedures developed by academic groups have been successful in improving the default algorithms provided by the Affymetrix system. In this article we present a solution to one of the preprocessing steps-background adjustment-based on a formal statistical framework. Our Solution greatly improves the performance of the technology in various practical applications. These arrays use short oligonucleotides to probe for genes in an RNA sample. Typically, each gene is represented by 11-20 pairs of oligonucleotide probes. The first component of these pairs is referred to as a perfect match probe and is designed to hybridize only with transcripts from the intended gene (i.e.. specific hybridization). However, hybridization by other sequences (i.e., nonspecific hybridization) is unavoidable. Furthermore. hybridization strengths are measured by a scanner that introduces optical noise. Therefore, the observed intensities need to be adjusted to give accurate measurements of specific hybridization. We have found that the default ad hoc adjustment, provided as part of the Affymetrix system can be improved through the use of estimators derived from a statistical model that uses probe sequence information. A final step in preprocessing is to summarize the probe-level data for each gene to define a measure of expression that represents the amount of the corresponding mRNA species. In this article we illustrate the practical consequences of not adjusting appropriately for the presence of nonspecific hybridization and provide a solution based on our background adjustment procedure. Software that computes our adjustment is available as part of the Bioconductor Project (http://bioconductor.org).