寡核苷酸微阵列的预处理统计方法综述。
A review of statistical methods for preprocessing oligonucleotide microarrays.
机构信息
Center for Statistical Sciences and Department of Community Health, Brown University, RI 02912, USA.
出版信息
Stat Methods Med Res. 2009 Dec;18(6):533-41. doi: 10.1177/0962280209351924.
Abstract
Microarrays have become an indispensable tool in biomedical research. This powerful technology not only makes it possible to quantify a large number of nucleic acid molecules simultaneously, but also produces data with many sources of noise. A number of preprocessing steps are therefore necessary to convert the raw data, usually in the form of hybridisation images, to measures of biological meaning that can be used in further statistical analysis. Preprocessing of oligonucleotide arrays includes image processing, background adjustment, data normalisation/transformation and sometimes summarisation when multiple probes are used to target one genomic unit. In this article, we review the issues encountered in each preprocessing step and introduce the statistical models and methods in preprocessing.
摘要
微阵列已成为生物医学研究中不可或缺的工具。这项强大的技术不仅使同时定量大量核酸分子成为可能，而且还产生了许多噪声源的数据。因此，需要进行一些预处理步骤，以便将原始数据（通常以杂交图像的形式）转换为可用于进一步统计分析的生物意义的度量。寡核苷酸阵列的预处理包括图像处理、背景调整、数据归一化/转换，以及当多个探针用于靶向一个基因组单元时的汇总。在本文中，我们回顾了每个预处理步骤中遇到的问题，并介绍了预处理中的统计模型和方法。
相似文献
1
A review of statistical methods for preprocessing oligonucleotide microarrays.寡核苷酸微阵列的预处理统计方法综述。
Stat Methods Med Res. 2009 Dec;18(6):533-41. doi: 10.1177/0962280209351924.
2
Statistical challenges in preprocessing in microarray experiments in cancer.癌症微阵列实验预处理中的统计学挑战。
Clin Cancer Res. 2008 Oct 1;14(19):5959-66. doi: 10.1158/1078-0432.CCR-07-4532.
3
Micro-Analyzer: automatic preprocessing of Affymetrix microarray data.微分析器：Affymetrix 微阵列数据的自动预处理。
Comput Methods Programs Biomed. 2013 Aug;111(2):402-9. doi: 10.1016/j.cmpb.2013.04.006. Epub 2013 May 31.
4
Unfolding of microarray data.微阵列数据的展开
J Comput Biol. 2001;8(4):443-61. doi: 10.1089/106652701752236232.
5
Preprocessing of oligonucleotide array data.寡核苷酸阵列数据的预处理。
Nat Biotechnol. 2004 Jun;22(6):656-8; author reply 658. doi: 10.1038/nbt0604-656b.
6
Working with Oligonucleotide Arrays.使用寡核苷酸阵列
Methods Mol Biol. 2016;1418:145-59. doi: 10.1007/978-1-4939-3578-9_7.
7
Statistical methods for microarray assays.微阵列分析的统计方法。
J Appl Genet. 2002;43(3):269-78.
8
A comprehensive overview of Infinium HumanMethylation450 data processing.Infinium HumanMethylation450 数据处理的全面概述。
Brief Bioinform. 2014 Nov;15(6):929-41. doi: 10.1093/bib/bbt054. Epub 2013 Aug 29.
9
mu-CS: an extension of the TM4 platform to manage Affymetrix binary data.mu-CS：TM4 平台的一个扩展，用于管理 Affymetrix 二进制数据。
BMC Bioinformatics. 2010 Jun 10;11:315. doi: 10.1186/1471-2105-11-315.
10
A model for measurement error for gene expression arrays.基因表达阵列测量误差模型。
J Comput Biol. 2001;8(6):557-69. doi: 10.1089/106652701753307485.
引用本文的文献
1
Identification of the Exercise and Time Effects on Human Skeletal Muscle through Bioinformatics Methods.通过生物信息学方法鉴定人类骨骼肌的运动和时间效应。
Genet Res (Camb). 2022 Aug 21;2022:9582363. doi: 10.1155/2022/9582363. eCollection 2022.
2
Decision Theory versus Conventional Statistics for Personalized Therapy of Breast Cancer.用于乳腺癌个体化治疗的决策理论与传统统计学
J Pers Med. 2022 Apr 2;12(4):570. doi: 10.3390/jpm12040570.
3
Decision theory for precision therapy of breast cancer.决策理论在乳腺癌精准治疗中的应用。
Sci Rep. 2021 Feb 19;11(1):4233. doi: 10.1038/s41598-021-82418-7.
4
The role of gene to gene interaction in the breast's genomic signature of pregnancy.基因间相互作用在妊娠乳腺基因组特征中的作用。
Sci Rep. 2021 Jan 29;11(1):2643. doi: 10.1038/s41598-021-81704-8.
5
Array Analysis Manager-An automated DNA microarray analysis tool simplifying microarray data filtering, bias recognition, normalization, and expression analysis.阵列分析管理器——一种自动化的DNA微阵列分析工具，可简化微阵列数据过滤、偏差识别、标准化和表达分析。
Eng Life Sci. 2017 Jun 12;17(8):841-846. doi: 10.1002/elsc.201700046. eCollection 2017 Aug.
6
Recent Trends, Technical Concepts and Components of Computer-Assisted Orthopedic Surgery Systems: A Comprehensive Review.计算机辅助骨科手术系统的最新趋势、技术概念和组成部分：全面综述。
Sensors (Basel). 2019 Nov 27;19(23):5199. doi: 10.3390/s19235199.
7
A Bootstrap Based Measure Robust to the Choice of Normalization Methods for Detecting Rhythmic Features in High Dimensional Data.一种基于自助法的度量，对用于检测高维数据中节律特征的归一化方法的选择具有鲁棒性。
Front Genet. 2018 Feb 2;9:24. doi: 10.3389/fgene.2018.00024. eCollection 2018.
8
Gene expression effects of glucocorticoid and mineralocorticoid receptor agonists and antagonists on normal human skeletal muscle.糖皮质激素和盐皮质激素受体激动剂及拮抗剂对正常人体骨骼肌的基因表达影响。
Physiol Genomics. 2017 Jun 1;49(6):277-286. doi: 10.1152/physiolgenomics.00128.2016. Epub 2017 Apr 21.
9
RNA-seq mixology: designing realistic control experiments to compare protocols and analysis methods.RNA测序混合技术：设计实际的对照实验以比较实验方案和分析方法。
Nucleic Acids Res. 2017 Mar 17;45(5):e30. doi: 10.1093/nar/gkw1063.
10
t-Test at the Probe Level: An Alternative Method to Identify Statistically Significant Genes for Microarray Data.探针水平的t检验：一种识别微阵列数据中具有统计学意义基因的替代方法。
Microarrays (Basel). 2014 Dec 16;3(4):340-51. doi: 10.3390/microarrays3040340.
本文引用的文献
1
Normalization of oligonucleotide arrays based on the least-variant set of genes.基于基因变异最小集的寡核苷酸阵列标准化
BMC Bioinformatics. 2008 Mar 5;9:140. doi: 10.1186/1471-2105-9-140.
2
Model-based variance-stabilizing transformation for Illumina microarray data.用于Illumina微阵列数据的基于模型的方差稳定变换
Nucleic Acids Res. 2008 Feb;36(2):e11. doi: 10.1093/nar/gkm1075. Epub 2008 Jan 4.
3
An overview of image-processing methods for Affymetrix GeneChips.Affymetrix基因芯片图像处理方法概述。
Brief Bioinform. 2008 Jan;9(1):25-33. doi: 10.1093/bib/bbm055. Epub 2007 Dec 5.
4
Exon arrays provide accurate assessments of gene expression.外显子阵列可提供基因表达的准确评估。
Genome Biol. 2007;8(5):R82. doi: 10.1186/gb-2007-8-5-r82.
5
Microarray blob-defect removal improves array analysis.微阵列斑点缺陷去除可改善阵列分析。
Bioinformatics. 2007 Apr 15;23(8):966-71. doi: 10.1093/bioinformatics/btm043. Epub 2007 Mar 1.
6
Model-based analysis of tiling-arrays for ChIP-chip.基于模型的染色质免疫沉淀芯片（ChIP-chip）平铺阵列分析
Proc Natl Acad Sci U S A. 2006 Aug 15;103(33):12457-62. doi: 10.1073/pnas.0601180103. Epub 2006 Aug 8.
7
Parameter estimation for the calibration and variance stabilization of microarray data.用于微阵列数据校准和方差稳定化的参数估计
Stat Appl Genet Mol Biol. 2003;2:Article3. doi: 10.2202/1544-6115.1008. Epub 2003 Apr 5.
8
Harshlight: a "corrective make-up" program for microarray chips.Harshlight：一种用于微阵列芯片的“校正性化妆”程序。 （此译文感觉不太符合常理，推测原文可能存在错误表述，正常可能想表达的是与芯片校正相关的程序，但按照要求逐字翻译就是这样。）
BMC Bioinformatics. 2005 Dec 10;6:294. doi: 10.1186/1471-2105-6-294.
9
Stochastic models inspired by hybridization theory for short oligonucleotide arrays.受短寡核苷酸阵列杂交理论启发的随机模型。
J Comput Biol. 2005 Jul-Aug;12(6):882-93. doi: 10.1089/cmb.2005.12.882.
10
A benchmark for Affymetrix GeneChip expression measures.Affymetrix基因芯片表达量测量的一个基准。
Bioinformatics. 2004 Feb 12;20(3):323-31. doi: 10.1093/bioinformatics/btg410.
Zotero 插件