Reproducible Research: A Bioinformatics Case Study
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Robert Gentleman
While scientific research and the methodologies involved have gone through substantial technological evolution the technology involved in the publication of the results of these endeavors has remained relatively stagnant. Publication is largely done in the same manner today as it was fifty years ago. Many journals have adopted electronic formats, however, their orientation and style is little different from a printed document. The documents tend to be static and take little advantage of computational resources that might be available. Recent work, Gentleman and Temple Lang (2003), suggests a methodology and basic infrastructure that can be used to publish documents in a substantially different way. Their approach is suitable for the publication of papers whose message relies on computation. Stated quite simply, Gentleman and Temple Lang (2003) propose a paradigm where documents are mixtures of code and text. Such documents may be self-contained or they may be a component of a compendium which provides the infrastructure needed to provide access to data and supporting software. These documents, or compendiums, can be processed in a number of different ways. One transformation will be to replace the code with its output -- thereby providing the familiar, but limited, static document. In this paper we apply these concepts to a seminal paper in bioinformatics, namely The Molecular Classification of Cancer, Golub et al (1999). The authors of that paper have generously provided data and other information that have allowed us to largely reproduce their results. Rather than reproduce this paper exactly we demonstrate that such a reproduction is possible and instead concentrate on demonstrating the usefulness of the compendium concept itself.
©2011 Walter de Gruyter GmbH & Co. KG, Berlin/Boston
Artikel in diesem Heft
- Article
- Estimating Motifs Under Order Restrictions
- Reproducible Research: A Bioinformatics Case Study
- Generalized Rank Tests for Replicated Microarray Data
- Stepwise Normalization of Two-Channel Spotted Microarrays
- Comparing Automatic and Manual Image Processing in FLARE Assay Analysis for Colon Carcinogenesis
- Pixel-level Signal Modelling with Spatial Correlation for Two-Colour Microarrays
- Empirical Bayes Microarray ANOVA and Grouping Cell Lines by Equal Expression Levels
- Multiple Testing and Data Adaptive Regression: An Application to HIV-1 Sequence Data.
- Early Diagnostic Marker Panel Determination for Microarray Based Clinical Studies
- Prediction of Missing Values in Microarray and Use of Mixed Models to Evaluate the Predictors
- Combined Association and Linkage Analysis for General Pedigrees and Genetic Models
- Incorporating Biological Information as a Prior in an Empirical Bayes Approach to Analyzing Microarray Data
- The Relative Inefficiency of Sequence Weights Approaches in Determining a Nucleotide Position Weight Matrix
- A Simple Loglinear Model for Haplotype Effects in a Case-Control Study Involving Two Unphased Genotypes
- Extension of the SIMLA Package for Generating Pedigrees with Complex Inheritance Patterns: Environmental Covariates, Gene-Gene and Gene-Environment Interaction
- Error Distribution for Gene Expression Data
- A General Framework for Weighted Gene Co-Expression Network Analysis
- Statistical Inference in Evolutionary Models of DNA Sequences via the EM Algorithm
- Comparing Bacterial DNA Microarray Fingerprints
- Continuous Covariates in Genetic Association Studies of Case-Parent Triads: Gene and Gene-Environment Interaction Effects, Population Stratification, and Power Analysis
- Robust Remote Homology Detection by Feature Based Profile Hidden Markov Models
- Empirical Bayes Estimation of a Sparse Vector of Gene Expression Changes
- Hierarchical Inverse Gaussian Models and Multiple Testing: Application to Gene Expression Data
- FADO: A Statistical Method to Detect Favored or Avoided Distances between Occurrences of Motifs using the Hawkes' Model
- Prediction of Genomewide Conserved Epitope Profiles of HIV-1: Classifier Choice and Peptide Representation
- Fold-Change Estimation of Differentially Expressed Genes using Mixture Mixed-Model
- Test on the Structure of Biological Sequences via Chaos Game Representation
- Reverse Engineering Galactose Regulation in Yeast through Model Selection
- Empirical Bayes and Resampling Based Multiple Testing Procedure Controlling Tail Probability of the Proportion of False Positives.
- Weighted Analysis of Paired Microarray Experiments
- A Probabilistic Approach to Large-Scale Association Scans: A Semi-Bayesian Method to Detect Disease-Predisposing Alleles
- A Shrinkage Approach to Large-Scale Covariance Matrix Estimation and Implications for Functional Genomics
- Structured Antedependence Models for Functional Mapping of Multiple Longitudinal Traits
- Correlation Between Gene Expression Levels and Limitations of the Empirical Bayes Methodology for Finding Differentially Expressed Genes
- Bayesian Statistical Studies of the Ramachandran Distribution
- On Reference Designs For Microarray Experiments
- Computing Asymptotic Power and Sample Size for Case-Control Genetic Association Studies in the Presence of Phenotype and/or Genotype Misclassification Errors
Artikel in diesem Heft
- Article
- Estimating Motifs Under Order Restrictions
- Reproducible Research: A Bioinformatics Case Study
- Generalized Rank Tests for Replicated Microarray Data
- Stepwise Normalization of Two-Channel Spotted Microarrays
- Comparing Automatic and Manual Image Processing in FLARE Assay Analysis for Colon Carcinogenesis
- Pixel-level Signal Modelling with Spatial Correlation for Two-Colour Microarrays
- Empirical Bayes Microarray ANOVA and Grouping Cell Lines by Equal Expression Levels
- Multiple Testing and Data Adaptive Regression: An Application to HIV-1 Sequence Data.
- Early Diagnostic Marker Panel Determination for Microarray Based Clinical Studies
- Prediction of Missing Values in Microarray and Use of Mixed Models to Evaluate the Predictors
- Combined Association and Linkage Analysis for General Pedigrees and Genetic Models
- Incorporating Biological Information as a Prior in an Empirical Bayes Approach to Analyzing Microarray Data
- The Relative Inefficiency of Sequence Weights Approaches in Determining a Nucleotide Position Weight Matrix
- A Simple Loglinear Model for Haplotype Effects in a Case-Control Study Involving Two Unphased Genotypes
- Extension of the SIMLA Package for Generating Pedigrees with Complex Inheritance Patterns: Environmental Covariates, Gene-Gene and Gene-Environment Interaction
- Error Distribution for Gene Expression Data
- A General Framework for Weighted Gene Co-Expression Network Analysis
- Statistical Inference in Evolutionary Models of DNA Sequences via the EM Algorithm
- Comparing Bacterial DNA Microarray Fingerprints
- Continuous Covariates in Genetic Association Studies of Case-Parent Triads: Gene and Gene-Environment Interaction Effects, Population Stratification, and Power Analysis
- Robust Remote Homology Detection by Feature Based Profile Hidden Markov Models
- Empirical Bayes Estimation of a Sparse Vector of Gene Expression Changes
- Hierarchical Inverse Gaussian Models and Multiple Testing: Application to Gene Expression Data
- FADO: A Statistical Method to Detect Favored or Avoided Distances between Occurrences of Motifs using the Hawkes' Model
- Prediction of Genomewide Conserved Epitope Profiles of HIV-1: Classifier Choice and Peptide Representation
- Fold-Change Estimation of Differentially Expressed Genes using Mixture Mixed-Model
- Test on the Structure of Biological Sequences via Chaos Game Representation
- Reverse Engineering Galactose Regulation in Yeast through Model Selection
- Empirical Bayes and Resampling Based Multiple Testing Procedure Controlling Tail Probability of the Proportion of False Positives.
- Weighted Analysis of Paired Microarray Experiments
- A Probabilistic Approach to Large-Scale Association Scans: A Semi-Bayesian Method to Detect Disease-Predisposing Alleles
- A Shrinkage Approach to Large-Scale Covariance Matrix Estimation and Implications for Functional Genomics
- Structured Antedependence Models for Functional Mapping of Multiple Longitudinal Traits
- Correlation Between Gene Expression Levels and Limitations of the Empirical Bayes Methodology for Finding Differentially Expressed Genes
- Bayesian Statistical Studies of the Ramachandran Distribution
- On Reference Designs For Microarray Experiments
- Computing Asymptotic Power and Sample Size for Case-Control Genetic Association Studies in the Presence of Phenotype and/or Genotype Misclassification Errors
