III The Science Behind HelixTree
Part III
The Science Behind HelixTree
26 Formulas and Theories
26.1 Split-Prediction Methodology
26.2 Normally Distributed Response Binomial Predictor
26.3 Normally Distributed Response Continuous-Ordinal Predictor
26.4 Normally Distributed Response Categorical Predictor
26.5 Linear Regression From a Tree Node
26.6 Haplotype Trend Regression (HTR) with Continuous Response
26.7 Composite Haplotype Method (CHM)
26.8 Haplotype Trend Regression (HTR) with Continuous Response and Covariates (Optional Module)
26.9 Stepwise Regression (Optional Module)
26.10 Categorical Covariates and Interaction Terms (Optional Module)
26.11 Results from Linear Regression (Optional Module)
26.12 Binomially Distributed Response Binary Predictor
26.13 Binomially Distributed Response Continuous/Ordinal Predictor
26.14 Binomially Distributed Response Categorical Predictor
26.15 Logistic Regression From a Tree Node
26.16 Haplotype Trend Regression (HTR) with Binomial Response
26.17 Haplotype Trend Regression (HTR) with Binomial Response and Covariates (Optional Module)
26.18 Results from Logistic Regression (Optional Module)
26.19 Categorical Response
26.20 The False Discovery Rate and the Simes Method
26.21 Permutation Test Methodology
26.22 Methods for the Genetic Association Tests
26.23 Formulas for Principal Components Analysis
26.24 Methods for Obtaining General Marker Statistics
A EULA
B Installing the Third-Party Condor
Package
B.1 Installing Condor
Overview
B.2 Downloading and Using the Installation Wizard
B.3 Troubleshooting Techniques and Common Issues
C Extracting Affymetrix Copy Number Data for use in HelixTree
C.1 Extracting Affymetrix Copy Number Data Overview
C.2 Creating CNT Files using the Affymetrix CNAT Batch Analysis Tool
C.3 Creating CNCHP Files using Affymetrix Genotyping Console 2.0
C.4 Affymetrix CNT File Format
D Exporting Data from BeadStudio
D.1 Exporting Data From BeadStudio Overview
D.2 Exporting Genotype Data using the BeadStudio Final Report
D.3 Exporting Copy Number Data using the HelixTree DSF Plug-In
E Platform Notes
E.1 Microsoft Windows
E.2 Linux
E.3 Mac OS X
F Bug Fix History
F.1 Bugs Fixed by Version
G Bibliography
Bibliography
26.1 Split-Prediction Methodology
26.2 Normally Distributed Response Binomial Predictor
26.3 Normally Distributed Response Continuous-Ordinal Predictor
26.4 Normally Distributed Response Categorical Predictor
26.5 Linear Regression From a Tree Node
26.6 Haplotype Trend Regression (HTR) with Continuous Response
26.7 Composite Haplotype Method (CHM)
26.8 Haplotype Trend Regression (HTR) with Continuous Response and Covariates (Optional Module)
26.9 Stepwise Regression (Optional Module)
26.10 Categorical Covariates and Interaction Terms (Optional Module)
26.11 Results from Linear Regression (Optional Module)
26.12 Binomially Distributed Response Binary Predictor
26.13 Binomially Distributed Response Continuous/Ordinal Predictor
26.14 Binomially Distributed Response Categorical Predictor
26.15 Logistic Regression From a Tree Node
26.16 Haplotype Trend Regression (HTR) with Binomial Response
26.17 Haplotype Trend Regression (HTR) with Binomial Response and Covariates (Optional Module)
26.18 Results from Logistic Regression (Optional Module)
26.19 Categorical Response
26.20 The False Discovery Rate and the Simes Method
26.21 Permutation Test Methodology
26.22 Methods for the Genetic Association Tests
26.23 Formulas for Principal Components Analysis
26.24 Methods for Obtaining General Marker Statistics
A EULA
B Installing the Third-Party Condor
Package
B.1 Installing Condor
Overview
B.2 Downloading and Using the Installation Wizard
B.3 Troubleshooting Techniques and Common Issues
C Extracting Affymetrix Copy Number Data for use in HelixTree
C.1 Extracting Affymetrix Copy Number Data Overview
C.2 Creating CNT Files using the Affymetrix CNAT Batch Analysis Tool
C.3 Creating CNCHP Files using Affymetrix Genotyping Console 2.0
C.4 Affymetrix CNT File Format
D Exporting Data from BeadStudio
D.1 Exporting Data From BeadStudio Overview
D.2 Exporting Genotype Data using the BeadStudio Final Report
D.3 Exporting Copy Number Data using the HelixTree DSF Plug-In
E Platform Notes
E.1 Microsoft Windows
E.2 Linux
E.3 Mac OS X
F Bug Fix History
F.1 Bugs Fixed by Version
G Bibliography
Bibliography
