NBLDA – negative binomial linear discriminant analysis for RNA-Seq data

RNA-sequencing (RNA-Seq) has become a powerful technology to characterize gene expression profiles because it is more accurate and comprehensive than microarrays. Although statistical methods that have been developed for microarray data can be applied to RNA-Seq data, they are not ideal due to the discrete nature of RNA-Seq data. The Poisson distribution and negative binomial distribution are commonly used to model count data. Recently, Witten (Annals Appl Stat 5:2493-2518, 2011) proposed a Poisson linear discriminant analysis for RNA-Seq data. The Poisson assumption may not be as appropriate as the negative binomial distribution when biological replicates are available and in the presence of overdispersion (i.e., when the variance is larger than or equal to the mean). However, it is more complicated to model negative binomial variables because they involve a dispersion parameter that needs to be estimated.

In this paper, researchers from Hong Kong Baptist University propose a negative binomial linear discriminant analysis for RNA-Seq data. By Bayes’ rule, they construct the classifier by fitting a negative binomial model, and propose some plug-in rules to estimate the unknown parameters in the classifier. The relationship between the negative binomial classifier and the Poisson classifier is explored, with a numerical investigation of the impact of dispersion on the discriminant score. Simulation results show the superiority of this proposed method. The researchers also analyze two real RNA-Seq data sets to demonstrate the advantages of our method in real-world applications.

rna-seq

Mean misclassification rates for real data sets

Availability – R code is available at http://www.comp.hkbu.edu.hk/~xwan/NBLDA.R

or https://github.com/yangchadam/NBLDA

Dong K, Zhao H, Tong T, Wan X. (2016) NBLDA: negative binomial linear discriminant analysis for RNA-Seq data. BMC Bioinformatics 17(1):369. [article]

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