Classification and clustering of sequencing data using a Poisson model
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Publication:765993
DOI10.1214/11-AOAS493zbMATH Open1234.62150arXiv1202.6201OpenAlexW3103302162MaRDI QIDQ765993FDOQ765993
Publication date: 22 March 2012
Published in: The Annals of Applied Statistics (Search for Journal in Brave)
Abstract: In recent years, advances in high throughput sequencing technology have led to a need for specialized methods for the analysis of digital gene expression data. While gene expression data measured on a microarray take on continuous values and can be modeled using the normal distribution, RNA sequencing data involve nonnegative counts and are more appropriately modeled using a discrete count distribution, such as the Poisson or the negative binomial. Consequently, analytic tools that assume a Gaussian distribution (such as classification methods based on linear discriminant analysis and clustering methods that use Euclidean distance) may not perform as well for sequencing data as methods that are based upon a more appropriate distribution. Here, we propose new approaches for performing classification and clustering of observations on the basis of sequencing data. Using a Poisson log linear model, we develop an analog of diagonal linear discriminant analysis that is appropriate for sequencing data. We also propose an approach for clustering sequencing data using a new dissimilarity measure that is based upon the Poisson model. We demonstrate the performances of these approaches in a simulation study, on three publicly available RNA sequencing data sets, and on a publicly available chromatin immunoprecipitation sequencing data set.
Full work available at URL: https://arxiv.org/abs/1202.6201
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Classification and discrimination; cluster analysis (statistical aspects) (62H30) Applications of statistics to biology and medical sciences; meta analysis (62P10) Biochemistry, molecular biology (92C40)
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Cited In (16)
- Variational discriminant analysis with variable selection
- Exact Bayesian designs for count time series
- Variational nonparametric discriminant analysis
- Clustering for multivariate continuous and discrete longitudinal data
- Dealing with overdispersion in multivariate count data
- Exponential-Family Embedding With Application to Cell Developmental Trajectories for Single-Cell RNA-Seq Data
- Two‐group Poisson‐Dirichlet mixtures for multiple testing
- PoiClaClu
- Simultaneous estimation of cluster number and feature sparsity in high‐dimensional cluster analysis
- Category encoding method to select feature genes for the classification of bulk and single-cell RNA-seq data
- A sparse negative binomial classifier with covariate adjustment for RNA-seq data
- Multiple suboptimal solutions for prediction rules in gene expression data
- Classification of RNA-Seq data via Gaussian copulas
- Discovering political topics in facebook discussion threads with graph contextualization
- Bayesian sparse multivariate regression with asymmetric nonlocal priors for microbiome data analysis
- Fast model-based clustering of partial records
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