Dataset Information

Distributed Simultaneous Inference in Generalized Linear Models via Confidence Distribution.

ABSTRACT: We propose a distributed method for simultaneous inference for datasets with sample size much larger than the number of covariates, i.e., N ? p, in the generalized linear models framework. When such datasets are too big to be analyzed entirely by a single centralized computer, or when datasets are already stored in distributed database systems, the strategy of divide-and-combine has been the method of choice for scalability. Due to partition, the sub-dataset sample sizes may be uneven and some possibly close to p, which calls for regularization techniques to improve numerical stability. However, there is a lack of clear theoretical justification and practical guidelines to combine results obtained from separate regularized estimators, especially when the final objective is simultaneous inference for a group of regression parameters. In this paper, we develop a strategy to combine bias-corrected lasso-type estimates by using confidence distributions. We show that the resulting combined estimator achieves the same estimation efficiency as that of the maximum likelihood estimator using the centralized data. As demonstrated by simulated and real data examples, our divide-and-combine method yields nearly identical inference as the centralized benchmark.

SUBMITTER: Tang L

PROVIDER: S-EPMC7453826 | biostudies-literature | 2020 Mar

REPOSITORIES: biostudies-literature

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Distributed Simultaneous Inference in Generalized Linear Models via Confidence Distribution.

Tang Lu L Zhou Ling L Song Peter X-K PX

Journal of multivariate analysis 20191128

We propose a distributed method for simultaneous inference for datasets with sample size much larger than the number of covariates, i.e., <i>N</i> ≫ <i>p</i>, in the generalized linear models framework. When such datasets are too big to be analyzed entirely by a single centralized computer, or when datasets are already stored in distributed database systems, the strategy of divide-and-combine has been the method of choice for scalability. Due to partition, the sub-dataset sample sizes may be une ...[more]

PMID: 32863459

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Project description:BackgroundTechnological advances involving RNA-Seq and Bioinformatics allow quantifying the transcriptional levels of genes in cells, tissues, and cell lines, permitting the identification of Differentially Expressed Genes (DEGs). DESeq2 and edgeR are well-established computational tools used for this purpose and they are based upon generalized linear models (GLMs) that consider only fixed effects in modeling. However, the inclusion of random effects reduces the risk of missing potential DEGs that may be essential in the context of the biological phenomenon under investigation. The generalized linear mixed models (GLMM) can be used to include both effects.MethodsWe present DEGRE (Differentially Expressed Genes with Random Effects), a user-friendly tool capable of inferring DEGs where fixed and random effects on individuals are considered in the experimental design of RNA-Seq research. DEGRE preprocesses the raw matrices before fitting GLMMs on the genes and the derived regression coefficients are analyzed using the Wald statistical test. DEGRE offers the Benjamini-Hochberg or Bonferroni techniques for P-value adjustment.ResultsThe datasets used for DEGRE assessment were simulated with known identification of DEGs. These have fixed effects, and the random effects were estimated and inserted to measure the impact of experimental designs with high biological variability. For DEGs' inference, preprocessing effectively prepares the data and retains overdispersed genes. The biological coefficient of variation is inferred from the counting matrices to assess variability before and after the preprocessing. The DEGRE is computationally validated through its performance by the simulation of counting matrices, which have biological variability related to fixed and random effects. DEGRE also provides improved assessment measures for detecting DEGs in cases with higher biological variability. We show that the preprocessing established here effectively removes technical variation from those matrices. This tool also detects new potential candidate DEGs in the transcriptome data of patients with bipolar disorder, presenting a promising tool to detect more relevant genes.ConclusionsDEGRE provides data preprocessing and applies GLMMs for DEGs' inference. The preprocessing allows efficient remotion of genes that could impact the inference. Also, the computational and biological validation of DEGRE has shown to be promising in identifying possible DEGs in experiments derived from complex experimental designs. This tool may help handle random effects on individuals in the inference of DEGs and presents a potential for discovering new interesting DEGs for further biological investigation.

Dataset Information

Distributed Simultaneous Inference in Generalized Linear Models via Confidence Distribution.

Publications

Distributed Simultaneous Inference in Generalized Linear Models via Confidence Distribution.

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