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Title: LFCseq: a nonparametric approach for differential expression analysis of RNA-seq data
Authors: Lin, Bingqing
Zhang, Li-Feng
Chen, Xin
Keywords: Differential expression
Issue Date: 2014
Source: Lin, B., Zhang, L.-F., & Chen, X. (2014). LFCseq: a nonparametric approach for differential expression analysis of RNA-seq data. BMC Genomics, 15(S7).
Series/Report no.: BMC Genomics
Abstract: Background: With the advances in high-throughput DNA sequencing technologies, RNA-seq has rapidly emerged as a powerful tool for the quantitative analysis of gene expression and transcript variant discovery. In comparative experiments, differential expression analysis is commonly performed on RNA-seq data to identify genes/features that are differentially expressed between biological conditions. Most existing statistical methods for differential expression analysis are parametric and assume either Poisson distribution or negative binomial distribution on gene read counts. However, violation of distributional assumptions or a poor estimation of parameters often leads to unreliable results. Results: In this paper, we introduce a new nonparametric approach called LFCseq that uses log fold changes as a differential expression test statistic. To test each gene for differential expression, LFCseq estimates a null probability distribution of count changes from a selected set of genes with similar expression strength. In contrast, the nonparametric NOISeq approach relies on a null distribution estimated from all genes within an experimental condition regardless of their expression levels. Conclusion: Through extensive simulation study and RNA-seq real data analysis, we demonstrate that the proposed approach could well rank the differentially expressed genes ahead of non-differentially expressed genes, thereby achieving a much improved overall performance for differential expression analysis.
ISSN: 1471-2164
DOI: 10.1186/1471-2164-15-S10-S7
Schools: School of Biological Sciences 
School of Physical and Mathematical Sciences 
Rights: © 2014 Lin et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver ( applies to the data made available in this article, unless otherwise stated.
Fulltext Permission: open
Fulltext Availability: With Fulltext
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