Data quality aware analysis of differential expression in RNA-seq with NOISeq R/Bioc package | Zendy

Sonia Tarazona | Zendy; Pedro FurióTarí | Zendy; David Turrà | Zendy; Antonio Di Pietro | Zendy; María José Nueda | Zendy; Alberto Ferrer | Zendy; Ana Conesa | Zendy

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Data quality aware analysis of differential expression in RNA-seq with NOISeq R/Bioc package

Author(s) -

Sonia Tarazona,

Pedro FurióTarí,

David Turrà,

Antonio Di Pietro,

María José Nueda,

Alberto Ferrer,

Ana Conesa

Publication year - 2015

Publication title -

nucleic acids research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.008

H-Index - 537

eISSN - 1362-4954

pISSN - 0305-1048

DOI - 10.1093/nar/gkv711

Subject(s) - false positive paradox , biology , replication (statistics) , rna seq , quality (philosophy) , computational biology , differential (mechanical device) , expression (computer science) , data mining , rna , computer science , artificial intelligence , genetics , gene expression , transcriptome , programming language , philosophy , epistemology , virology , gene , engineering , aerospace engineering

As the use of RNA-seq has popularized, there is an increasing consciousness of the importance of experimental design, bias removal, accurate quantification and control of false positives for proper data analysis. We introduce the NOISeq R-package for quality control and analysis of count data. We show how the available diagnostic tools can be used to monitor quality issues, make pre-processing decisions and improve analysis. We demonstrate that the non-parametric NOISeqBIO efficiently controls false discoveries in experiments with biological replication and outperforms state-of-the-art methods. NOISeq is a comprehensive resource that meets current needs for robust data-aware analysis of RNA-seq differential expression.European Union Seventh Framework Programme [FP7/2007-2013, 306000]; Spanish Ministry of Science and Innovation [MICINN, BIO2008-04638-E], in the framework of ERA-Net Pathogenomics; MICINN [DPI2008-06880-C03-03/DPI]. Funding for open access charge: University of Florida, Publication Funds

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