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Nucleic Acids Res. 2015 Dec 2;43(21):e140. doi: 10.1093/nar/gkv711. Epub 2015 Jul 16.

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

Author information

1
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.
2
Genomics of Gene Expression Lab, Centro de Investigación Príncipe Felipe, Eduardo Primo Yúfera 3, 46012, Valencia, Spain.
3
Department of Genetics, Universidad de Córdoba, Campus de Rabanales Edificio Gregor Mendel, 14071, Córdoba, Spain.
4
Statistics and Operational Research Department, Universidad de Alicante, Carretera San Vicente del Raspeig s/n, 03690, Alicante, Spain.
5
Department of Applied Statistics, Operations Research and Quality, Universidad Politécnica de Valencia, Camí de Vera, 46022, Valencia, Spain.
6
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 aconesa@cipf.es.

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.

PMID:
26184878
PMCID:
PMC4666377
DOI:
10.1093/nar/gkv711
[Indexed for MEDLINE]
Free PMC Article

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