Detecting and correcting systematic variation in large-scale RNA sequencing data.
Detecting and correcting systematic variation in large-scale RNA sequencing data.
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DOI：
10.1038/nbt.3000
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发表时间：
2014-09
影响因子：
46.9
通讯作者：
Mason, Christopher E.
中科院分区：
文献类型：
--
作者：
Li, Sheng;Labaj, Pawel P.;Zumbo, Paul;Sykacek, Peter;Shi, Wei;Shi, Leming;Phan, John;Wu, Po-Yen;Wang, May;Wang, Charles;Thierry-Mieg, Danielle;Thierry-Mieg, Jean;Kreil, David P.;Mason, Christopher E.
High-throughput RNA sequencing (RNA-seq) enables comprehensive scans of entire transcriptomes, but best practices for analyzing RNA-seq data have not been fully defined, particularly for data collected with multiple sequencing platforms or at multiple sites. Here we used standardized RNA samples with built-in controls to examine sources of error in large-scale RNA-seq studies and their impact on the detection of differentially expressed genes (DEGs). Analysis of variations in guanine-cytosine content, gene coverage, sequencing error rate and insert size allowed identification of methods that produce more false positives or are less reproducible across sites. Moreover, commonly used methods fornormalization (cqn, EDASeq, RUV2, sva, PEER) varied in their ability to remove these systematic biases, depending on sample complexity and initial data quality. Normalization methods that combine data from genes across sites are strongly recommended to identify and remove site-specific effects, and can substantially improve RNA-seq studies.
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DOI：
10.1093/bioinformatics/btr247
发表时间：
2011-07-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Łabaj PP;Leparc GG;Linggi BE;Markillie LM;Wiley HS;Kreil DP
通讯作者：
Kreil DP
DOI：
10.1093/biostatistics/kxr054
发表时间：
2012-04
期刊：
Biostatistics (Oxford, England)
影响因子：
--
作者：
Hansen KD;Irizarry RA;Wu Z
通讯作者：
Wu Z
DOI：
10.1093/bioinformatics/btu638
发表时间：
2015-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Anders S;Pyl PT;Huber W
通讯作者：
Huber W
影响因子：
14.9
作者：
Hansen KD;Brenner SE;Dudoit S
通讯作者：
Dudoit S
影响因子：
4.3
作者：
Bragg LM;Stone G;Butler MK;Hugenholtz P;Tyson GW
通讯作者：
Tyson GW