Dataset Information

Robust Estimation of the Parameters of g - and - h Distributions, with Applications to Outlier Detection.

ABSTRACT: The g - and - h distributional family is generated from a relatively simple transformation of the standard normal and can approximate a broad spectrum of distributions. Consequently, it is easy to use in simulation studies and has been applied in multiple areas, including risk management, stock return analysis and missing data imputation studies. A rapidly convergent quantile based least squares (QLS) estimation method to fit the g - and - h distributional family parameters is proposed and then extended to a robust version. The robust version is then used as a more general outlier detection approach. Several properties of the QLS method are derived and comparisons made with competing methods through simulation. Real data examples of microarray and stock index data are used as illustrations.

SUBMITTER: Xu Y

PROVIDER: S-EPMC3961718 | biostudies-literature | 2014 Jul

REPOSITORIES: biostudies-literature

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Robust Estimation of the Parameters of g - and - h Distributions, with Applications to Outlier Detection.

Xu Yihuan Y Iglewicz Boris B Chervoneva Inna I

Computational statistics & data analysis 20140701

The g - and - h distributional family is generated from a relatively simple transformation of the standard normal and can approximate a broad spectrum of distributions. Consequently, it is easy to use in simulation studies and has been applied in multiple areas, including risk management, stock return analysis and missing data imputation studies. A rapidly convergent quantile based least squares (QLS) estimation method to fit the g - and - h distributional family parameters is prop ...[more]

PMID: 24665144

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Project description:BACKGROUND:High throughput RNA sequencing is a powerful approach to study gene expression. Due to the complex multiple-steps protocols in data acquisition, extreme deviation of a sample from samples of the same treatment group may occur due to technical variation or true biological differences. The high-dimensionality of the data with few biological replicates make it challenging to accurately detect those samples, and this issue is not well studied in the literature currently. Robust statistics is a family of theories and techniques aim to detect the outliers by first fitting the majority of the data and then flagging data points that deviate from it. Robust statistics have been widely used in multivariate data analysis for outlier detection in chemometrics and engineering. Here we apply robust statistics on RNA-seq data analysis. RESULTS:We report the use of two robust principal component analysis (rPCA) methods, PcaHubert and PcaGrid, to detect outlier samples in multiple simulated and real biological RNA-seq data sets with positive control outlier samples. PcaGrid achieved 100% sensitivity and 100% specificity in all the tests using positive control outliers with varying degrees of divergence. We applied rPCA methods and classical principal component analysis (cPCA) on an RNA-Seq data set profiling gene expression of the external granule layer in the cerebellum of control and conditional SnoN knockout mice. Both rPCA methods detected the same two outlier samples but cPCA failed to detect any. We performed differentially expressed gene detection before and after outlier removal as well as with and without batch effect modeling. We validated gene expression changes using quantitative reverse transcription PCR and used the result as reference to compare the performance of eight different data analysis strategies. Removing outliers without batch effect modeling performed the best in term of detecting biologically relevant differentially expressed genes. CONCLUSIONS:rPCA implemented in the PcaGrid function is an accurate and objective method to detect outlier samples. It is well suited for high-dimensional data with small sample sizes like RNA-seq data. Outlier removal can significantly improve the performance of differential gene detection and downstream functional analysis.

Dataset Information

Robust Estimation of the Parameters of g - and - h Distributions, with Applications to Outlier Detection.

Publications

Robust Estimation of the Parameters of <i>g - and - h</i> Distributions, with Applications to Outlier Detection.

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