ExactDAS: An Exact Test Procedure for the Detection of Differential Alternative Splicing in Microarray Experiments
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Tristan Mary-Huard
Abstract
The aim of this paper is to propose a test procedure for the detection of differential alternative splicing across conditions for tiling array or exon chip data. While developed in a mixed model framework, the test procedure is exact (avoiding computational burden) and applicable to a large variety of contrasts, including several previously published ones. A simulation study is presented to evaluate the robustness and performance of the method. It is found to have a good detection power of genes under differential alternative splicing, even for five biological replicates and four probes per exon. The methodology also enables the comparison of various experimental designs through exact power curves. This is illustrated with the comparison of paired and unpaired experiments. The test procedure was applied to two publicly available cancer data sets based on exon arrays, and showed promising results.
©2012 Walter de Gruyter GmbH & Co. KG, Berlin/Boston
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- ExactDAS: An Exact Test Procedure for the Detection of Differential Alternative Splicing in Microarray Experiments
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- Genotype Copy Number Variations using Gaussian Mixture Models: Theory and Algorithms
- Estimators of the local false discovery rate designed for small numbers of tests
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Articles in the same Issue
- Article
- Large-scale Parentage Inference with SNPs: an Efficient Algorithm for Statistical Confidence of Parent Pair Allocations
- ExactDAS: An Exact Test Procedure for the Detection of Differential Alternative Splicing in Microarray Experiments
- Incorporating Genomic Annotation into a Hidden Markov Model for DNA Methylation Tiling Array Data
- Variational Bayes Procedure for Effective Classification of Tumor Type with Microarray Gene Expression Data
- Detecting Differential Expression in RNA-sequence Data Using Quasi-likelihood with Shrunken Dispersion Estimates
- Empirical Bayesian Selection of Hypothesis Testing Procedures for Analysis of Sequence Count Expression Data
- Analyzing Genetic Association Studies with an Extended Propensity Score Approach
- Genotype Copy Number Variations using Gaussian Mixture Models: Theory and Algorithms
- Estimators of the local false discovery rate designed for small numbers of tests
- A PAUC-based Estimation Technique for Disease Classification and Biomarker Selection
- Comparison of Targeted Maximum Likelihood and Shrinkage Estimators of Parameters in Gene Networks
- DNA Pooling and Statistical Tests for the Detection of Single Nucleotide Polymorphisms
