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PMID: 26184878 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

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

Nucleic acids research ·Vol. 43 ·No. 21 ·2015-12-02 ·Pages e140

Tarazona S, Furió-Tarí P, Turrà D, Pietro AD, Nueda MJ, Ferrer A, Conesa A

Abstract

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.

MeSH Terms
Cell Line Data Interpretation, Statistical Gene Expression Profiling/standards Humans Male Prostatic Neoplasms/genetics Quality Control Sequence Analysis, RNA/standards Software
Authors & Affiliations
7 authors, click to expand affiliations / ORCID
Tarazona Sonia
Genomics of Gene Expression Lab, Centro de Investigación Príncipe Felipe, Eduardo Primo Yúfera 3, 46012, Valencia, Spain Department of Applied Statistics, Operations Research and Quality, Universidad Politécnica de Valencia, Camí de Vera, 46022, Valencia, Spain.
Furió-Tarí Pedro
Genomics of Gene Expression Lab, Centro de Investigación Príncipe Felipe, Eduardo Primo Yúfera 3, 46012, Valencia, Spain.
Turrà David
Department of Genetics, Universidad de Córdoba, Campus de Rabanales Edificio Gregor Mendel, 14071, Córdoba, Spain.
Pietro Antonio Di
Department of Genetics, Universidad de Córdoba, Campus de Rabanales Edificio Gregor Mendel, 14071, Córdoba, Spain.
Nueda María José
Statistics and Operational Research Department, Universidad de Alicante, Carretera San Vicente del Raspeig s/n, 03690, Alicante, Spain.
Ferrer Alberto
Department of Applied Statistics, Operations Research and Quality, Universidad Politécnica de Valencia, Camí de Vera, 46022, Valencia, Spain.
Conesa Ana
Genomics of Gene Expression Lab, Centro de Investigación Príncipe Felipe, Eduardo Primo Yúfera 3, 46012, Valencia, Spain Microbiology and Cell Science Department, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, FL 32603, USA [email protected].
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkv711
Email
[email protected]
Published
2015-12-02
Epub
2015-00-16
Pages
e140
Language
English
Region
England
NLM ID
0411011
PMCID
PMC4666377
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/gkv711 PMC Full Text View journal details
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