A Compendium to Ensure Computational Reproducibility in High-Dimensional Classification Tasks

Articles in the same Issue

1. Article
2. Using Alpha Wisely: Improving Power to Detect Multiple QTL
3. Relating HIV-1 Sequence Variation to Replication Capacity via Trees and Forests
4. Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments
5. Asymptotic Optimality of Likelihood-Based Cross-Validation
6. Using Importance Sampling to Improve Simulation in Linkage Analysis
7. Model-Based Assignment and Inference of Protein Backbone Nuclear Magnetic Resonances
8. Error-Rate and Decision-Theoretic Methods of Multiple Testing: Which Genes Have High Objective Probabilities of Differential Expression?
9. Evaluation of Multiple Models to Distinguish Closely Related Forms of Disease Using DNA Microarray Data: an Application to Multiple Myeloma
10. Saturation and Quantization Reduction in Microarray Experiments using Two Scans at Different Sensitivities
11. Combining Nearest Neighbor Classifiers Versus Cross-Validation Selection
12. Multiple Testing. Part I. Single-Step Procedures for Control of General Type I Error Rates
13. Multiple Testing. Part II. Step-Down Procedures for Control of the Family-Wise Error Rate
14. Augmentation Procedures for Control of the Generalized Family-Wise Error Rate and Tail Probabilities for the Proportion of False Positives
15. Calculating the Statistical Significance of Changes in Pathway Activity From Gene Expression Data
16. A Family-Based Association Test for Repeatedly Measured Quantitative Traits Adjusting for Unknown Environmental and/or Polygenic Effects
17. Deletion/Substitution/Addition Algorithm in Learning with Applications in Genomics
18. Classifying Gene Expression Profiles from Pairwise mRNA Comparisons
19. Hierarchical Bayesian Neural Network for Gene Expression Temporal Patterns
20. A Mixed Model Approach to Identify Yeast Transcriptional Regulatory Motifs via Microarray Experiments
21. Mammalian Genomes Ease Location of Human DNA Functional Segments but Not Their Description
22. On the Dependence Structure of Sequence Alignment Scores Calculated with Multiple Scoring Matrices
23. Increasing Power for Tests of Genetic Association in the Presence of Phenotype and/or Genotype Error by Use of Double-Sampling
24. A Method for Evaluating the Impact of Individual Haplotypes on Disease Incidence in Molecular Epidemiology Studies
25. Statistical Methods for Identifying Conserved Residues in Multiple Sequence Alignment
26. MergeMaid: R Tools for Merging and Cross-Study Validation of Gene Expression Data
27. Sparse Inverse of Covariance Matrix of QTL Effects with Incomplete Marker Data
28. Maximum Likelihood for Genome Phylogeny on Gene Content
29. Confidence Levels for the Comparison of Microarray Experiments
30. PLS Dimension Reduction for Classification with Microarray Data
31. Statistical Analysis of Genomic Tag Data
32. Statistical Analysis of Adsorption Models for Oligonucleotide Microarrays
33. Statistical Significance Threshold Criteria For Analysis of Microarray Gene Expression Data
34. A Compendium to Ensure Computational Reproducibility in High-Dimensional Classification Tasks
35. Validation and Discovery in Markov Models of Genetics Data
36. Making Sense of High-Throughput Protein-Protein Interaction Data
37. Reader's Reaction
38. Reader Reaction
39. Response to Foulkes and De Gruttola
40. Software Communication
41. BayesMendel: an R Environment for Mendelian Risk Prediction
42. Letter to the Editor
43. Concerns About Unreliable Data from Spotted cDNA Microarrays Due to Cross-Hybridization and Sequence Errors