title: ABSSeq: a new RNA-Seq analysis method based on modelling absolute expression differences.
abstract: The recent advances in next generation sequencing technology have made the sequencing of RNA (i.e., RNA-Seq) an extemely popular approach for gene expression analysis. Identification of significant differential expression represents a crucial initial step in these analyses, on which most subsequent inferences of biological functions are built. Yet, for identification of these subsequently analysed genes, most studies use an additional minimal threshold of differential expression that is not captured by the applied statistical procedures.
  
  
  
  Here we introduce a new analysis approach, ABSSeq, which uses a negative binomal distribution to model absolute expression differences between conditions, taking into account variations across genes and samples as well as magnitude of differences. In comparison to alternative methods, ABSSeq shows higher performance on controling type I error rate and at least a similar ability to correctly identify differentially expressed genes.
  
  
  
  ABSSeq specifically considers the overall magnitude of expression differences, which enhances the power in detecting truly differentially expressed genes by reducing false positives at both very low and high expression level. In addition, ABSSeq offers to calculate shrinkage of fold change to facilitate gene ranking and effective outlier detection.
authors.affiliation: Evolutionary Ecology and Genetics, Zoological Institute, CAU Kiel, Am Botanischen Garten 9, 24118, Kiel, Germany. wyang@zoologie.uni-kiel.de.
authors.forename: Wentao
authors.initials: W
authors.lastname: Yang
authors.affiliation: Centre for Molecular Biology, Institute for Clinical Molecular Biology, CAU Kiel, Am Botanischen Garten 11, 24118, Kiel, Germany.
authors.forename: Philip C
authors.initials: PC
authors.lastname: Rosenstiel
authors.affiliation: Evolutionary Ecology and Genetics, Zoological Institute, CAU Kiel, Am Botanischen Garten 9, 24118, Kiel, Germany. hschulenburg@zoologie.uni-kiel.de.
authors.forename: Hinrich
authors.initials: H
authors.lastname: Schulenburg
mesh_terms: D019295:Computational Biology / Q000379:methods; D003198:Computer Simulation; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation; D012372:ROC Curve; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software; D059467:Transcriptome
keywords: ABSSeq; Differential gene expression; Negative binomial distribution; RNA-Seq; Transcriptome analysis