NanoStringNorm: an extensible R package for the pre-processing of NanoString mRNA and miRNA data.
NanoStringNorm: an extensible R package for the pre-processing of NanoString mRNA and miRNA data.
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DOI：
10.1093/bioinformatics/bts188
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发表时间：
2012-06-01
期刊：
影响因子：
--
通讯作者：
Boutros PC
中科院分区：
文献类型：
--
作者：
Waggott D;Chu K;Yin S;Wouters BG;Liu FF;Boutros PC
研究动机：纳米链计数器平台是一种很有前途的新型核酸丰度测量技术。与基于pcr的技术相比，它有几个优点，包括避免扩增，直接序列询问和绝对定量的数字检测。这些特点最大限度地减少了实验误差，并有望处理具有挑战性的实验条件，如档案福尔马林固定石蜡包埋样品。然而，必须消除由样品保存、生物分子提取和平台波动的可变性引起的系统性样品间技术伪影，以确保数据的鲁棒性。结果：为了简化这个过程并解决NanoString数据集的这些问题，我们用R统计语言编写了一个名为NanoStringNorm的预处理包。主要功能包括可扩展的方法比较和新算法开发环境，集成基因和样本诊断，以及便利的下游统计分析。该软件包是开源的，可通过CRAN软件包存储库获得，包含单元测试以确保数值准确性，并提供可视化和数值诊断。可用性：http://cran.r-project.org/web/packages/NanoStringNorm联系方式：paul.boutros@oicr.on.ca补充信息：补充数据可在Bioinformatics在线获取。
Motivation: The NanoString nCounter Platform is a new and promising technology for measuring nucleic acid abundances. It has several advantages over PCR-based techniques, including avoidance of amplification, direct sequence interrogation and digital detection for absolute quantification. These features minimize aspects of experimental error and hold promise for dealing with challenging experimental conditions such as archival formalin-fixed paraffin-embedded samples. However, systematic inter-sample technical artifacts caused by variability in sample preservation, bio-molecular extraction and platform fluctuations must be removed to ensure robust data. Results: To facilitate this process and to address these issues for NanoString datasets, we have written a pre-processing package called NanoStringNorm in the R statistical language. Key features include an extensible environment for method comparison and new algorithm development, integrated gene and sample diagnostics, and facilitated downstream statistical analysis. The package is open-source, is available through the CRAN package repository, includes unit-tests to ensure numerical accuracy, and provides visual and numeric diagnostics. Availability: http://cran.r-project.org/web/packages/NanoStringNorm Contact: paul.boutros@oicr.on.ca Supplementary information: Supplementary data are available at Bioinformatics online.
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影响因子：
12.3
作者：
Gentleman RC;Carey VJ;Bates DM;Bolstad B;Dettling M;Dudoit S;Ellis B;Gautier L;Ge Y;Gentry J;Hornik K;Hothorn T;Huber W;Iacus S;Irizarry R;Leisch F;Li C;Maechler M;Rossini AJ;Sawitzki G;Smith C;Smyth G;Tierney L;Yang JY;Zhang J
通讯作者：
Zhang J
影响因子：
5
作者：
Hui, Angela B. Y.;Shi, Wei;Liu, Fei-Fei
通讯作者：
Liu, Fei-Fei
影响因子：
1.8
作者：
McCullough, B. D.;Heiser, David A.
通讯作者：
Heiser, David A.
影响因子：
3
作者：
Chen H;Boutros PC
通讯作者：
Boutros PC
影响因子：
46.9
作者：
Geiss, Gary K.;Bumgarner, Roger E.;Hood, Leroy
通讯作者：
Hood, Leroy