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原始副本：使用Affymetrix阵列改进拷贝数分析。

Rawcopy: Improved copy number analysis with Affymetrix arrays.

作者信息

Mayrhofer Markus, Viklund Björn, Isaksson Anders

机构信息

Science for Life Laboratory, Department of Medical Sciences, Uppsala University, SE-751 85 Uppsala, Sweden.

Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Nobels Väg 12A, SE-17177, Stockholm, Sweden.

出版信息

Sci Rep. 2016 Oct 31;6:36158. doi: 10.1038/srep36158.

DOI:10.1038/srep36158
PMID:27796336
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5086940/
Abstract

Microarray data is subject to noise and systematic variation that negatively affects the resolution of copy number analysis. We describe Rawcopy, an R package for processing of Affymetrix CytoScan HD, CytoScan 750k and SNP 6.0 microarray raw intensities (CEL files). Noise characteristics of a large number of reference samples are used to estimate log ratio and B-allele frequency for total and allele-specific copy number analysis. Rawcopy achieves better signal-to-noise ratio and higher proportion of validated alterations than commonly used free and proprietary alternatives. In addition, Rawcopy visualizes each microarray sample for assessment of technical quality, patient identity and genome-wide absolute copy number states. Software and instructions are available at http://rawcopy.org.

摘要

微阵列数据易受噪声和系统变异的影响，这会对拷贝数分析的分辨率产生负面影响。我们介绍了Rawcopy，这是一个用于处理Affymetrix CytoScan HD、CytoScan 750k和SNP 6.0微阵列原始强度（CEL文件）的R包。大量参考样本的噪声特征用于估计总拷贝数和等位基因特异性拷贝数分析的对数比率和B等位基因频率。与常用的免费和专有工具相比，Rawcopy实现了更好的信噪比和更高比例的经过验证的改变。此外，Rawcopy可视化每个微阵列样本，以评估技术质量、患者身份和全基因组绝对拷贝数状态。软件和说明可在http://rawcopy.org获取。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/06a8/5086940/6aaceb3b5016/srep36158-f8.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/06a8/5086940/58929755f0d0/srep36158-f1.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/06a8/5086940/f91cd9410de2/srep36158-f4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/06a8/5086940/8c9efbb84d9f/srep36158-f5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/06a8/5086940/8b6c80231c12/srep36158-f6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/06a8/5086940/8d98253e9511/srep36158-f7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/06a8/5086940/6aaceb3b5016/srep36158-f8.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/06a8/5086940/58929755f0d0/srep36158-f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/06a8/5086940/6d4532ec3267/srep36158-f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/06a8/5086940/9351fb17c0cb/srep36158-f3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/06a8/5086940/f91cd9410de2/srep36158-f4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/06a8/5086940/8c9efbb84d9f/srep36158-f5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/06a8/5086940/8b6c80231c12/srep36158-f6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/06a8/5086940/8d98253e9511/srep36158-f7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/06a8/5086940/6aaceb3b5016/srep36158-f8.jpg

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