fRMA ST：用于 Affymetrix Exon 和 Gene ST 阵列的冷冻稳健多阵列分析。
fRMA ST: frozen robust multiarray analysis for Affymetrix Exon and Gene ST arrays.
机构信息
Department of Biostatistics and Computational Biology, University of Rochester Medical Center, 265 Crittenden Blvd., CU 420630, Rochester, NY 14642, USA.
出版信息
Bioinformatics. 2012 Dec 1;28(23):3153-4. doi: 10.1093/bioinformatics/bts588. Epub 2012 Oct 7.
Abstract
SUMMARY
Frozen robust multiarray analysis (fRMA) is a single-array preprocessing algorithm that retains the advantages of multiarray algorithms and removes certain batch effects by downweighting probes that have high between-batch residual variance. Here, we extend the fRMA algorithm to two new microarray platforms--Affymetrix Human Exon and Gene 1.0 ST--by modifying the fRMA probe-level model and extending the frma package to work with oligo ExonFeatureSet and GeneFeatureSet objects.
AVAILABILITY AND IMPLEMENTATION
All packages are implemented in R. Source code and binaries are freely available through the Bioconductor project. Convenient links to all software and data packages can be found at http://mnmccall.com/software
CONTACT
摘要
摘要
冷冻稳健多阵列分析（fRMA）是一种单数组预处理算法，它保留了多阵列算法的优势，并通过降低具有高批次间残差方差的探针的权重来消除某些批次效应。在这里，我们通过修改 fRMA 探针级模型并扩展 frma 包以与 oligo ExonFeatureSet 和 GeneFeatureSet 对象配合使用，将 fRMA 算法扩展到两个新的微阵列平台——Affymetrix Human Exon 和 Gene 1.0 ST。
可用性和实现
所有软件包均在 R 中实现。源代码和二进制文件可通过 Bioconductor 项目免费获得。所有软件和数据包的便捷链接可在 http://mnmccall.com/software 找到。
联系方式
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本文引用的文献
1
Thawing Frozen Robust Multi-array Analysis (fRMA).解冻冷冻稳健多阵列分析（fRMA）。
BMC Bioinformatics. 2011 Sep 16;12:369. doi: 10.1186/1471-2105-12-369.
2
A framework for oligonucleotide microarray preprocessing.寡核苷酸微阵列预处理框架。
Bioinformatics. 2010 Oct 1;26(19):2363-7. doi: 10.1093/bioinformatics/btq431. Epub 2010 Aug 5.
3
Frozen robust multiarray analysis (fRMA).冻融稳健多阵列分析（fRMA）。
Biostatistics. 2010 Apr;11(2):242-53. doi: 10.1093/biostatistics/kxp059. Epub 2010 Jan 22.
4
Differential splicing using whole-transcript microarrays.使用全转录本微阵列进行差异剪接分析。
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