General Information
TM4 Software Overview
Starting MultiExperiment Viewer: Using Java Webstart
Loading Expression Data: Using the Annotation Feature; Initial View of the Loaded Data, Main Expression Image; Result Navigation Tree; The History Node and Log; MeV and other TIGR Files; Affymetrix Files; Gene Expression Omnibus (GEO) Files; MAGE-TAB Files; Genepix Files; Agilent Files; RNASeq Data Files
Adjusting the Data: Adjustment/Filter Overview; Data Transformations; Data Source Selection
Display Options: Sample Annotations; Selecting Gene Annotation; Color Scheme Selection; Setting Color Scale Limits; Element Apperance
Viewer Descriptions: Overview; Expression Images; Expression Graphs; Centroid Graphs; Table Views; Venn Diagrams; Expression Charts; Common Viewer Activities
Working with Clusters: Storing Clusters and Using the Cluster Manager
Utilities Menu: Search Utility; Import Gene or Sample List; Append Sample Annotation; Append Gene Annotation
Creating Output: Saving the Analysis; Saving the Expression Matrix; Saving Viewer Images; Saving Cluster Data
The Gaggle Implementation: Introduction to the Gaggle; The Gaggle Menu; Using the Gaggle with MeV
Modules: Description Conventions and General Pointers
HCL: Hierarchical Clustering: HCL Parameters; Adjusting the Tree Configuration and Viewing Clusters
TEASE: Tree-Ease: Mode selection; TEASE Parameters; Navigating the Hierarchical Tree; Adjusting Tree Configuration and Viewing Clusters
ST: Support Trees: Parameters
SOTA: Self Organizing Tree Algorithm: Parameters and Basic Terminology
KMC: K-Means/K-Medians Clustering: Parameters
KMS: K-Means/K-Medians Support: Parameters
CAST: Clustering Affinity Search Technique: Parameters
FOM: FOM-Figures of Merit
QTC: QT Cluster: Parameters
SOM: Self Organizing Maps: Basic Terminology; Parameters
NMF: Non-negative Matrix Factorization: Parameters
PTM: Template Matching: Parameters
TTEST: T-tests: Parameters
SAM: Significance Analysis of Microarrays: Parameters
ANOVA: Analysis of Variance: Parameters
TFA: Two-factor ANOVA
NonpaR: Nonparametric Statistical Tests: Brief Test Descriptions; Running NonpaR Tests; Mack-Skillings (MS) Test Dialogs; Fisher Exact Test
BETR: Bayesian Estimation of Temporal Regulation: Parameters
LIMMA: Linear Models for Microarray Data
GOSeq: Gene Ontology Analysis for RNASeq
SURV: Survival Analysis: Running the Module
GLOBANC: Global Analysis of Covariance
RP: Rank Products: Running the Module; Parameters
MINET: Mutual Information Network
EdgeR: Empirical Analysis of RNASeq Data in R
DeSEQ: Analysis of RNASeq Data based on Negative Binomial Distribution
DEGSEQ: Analysis of RNASeq Data based on MA Plot
SVM: Support Vector Machines: SVM Dialog Overview; Process Initialization Parameter Information; SVM Output
USC: Uncorrelated Shrunken Centroids: Advanced Parameters
KNNC: K-Nearest-Neighbor Classification: KNN Classification Parameter Information
DAM: Discriminant Analysis Module: Parameters
RN: Relevance Networks: Parameters
PCA: Principal Components Analysis
COA: Correspondence Analysis
TRN:Expression Terrain Maps: Terrain Navigation; The Terrain Viewer Menu; Cluster Selection and Related Operations
GSEA:Gene Set Enrichment Analysis
ATTR:Attract Package
EASE: Expression Analysis Systematic Explorer: Parameters; Advanced Parameters Dialog; Statistical Parameters Dialog
LEM: Linear Expression Maps
GDM: Gene Distance Matrix: Matrix Viewer Basics
BN: Bayesian Networks Analysis
LM:Literature Mining Analysis
GSH: Gene Shaving
Scripting: The Script; Diversity Variance Filter; Centroid Variance Filter
Comparative Genomic Hybridization Viewer: Loading Experiments; CGH Analyzer Viewers; The CGH Position Graph; The CGH Browser; CGH Analysis; Higher Level Analysis
Appendix: File Format Descriptions: TAV Files; Tab Delimited, Multiple Sample Files (TDMS files); GenePix Files; MEV Files; Annotation Files (.ann); Bioconductor (MAS5) Files; Affymetrix GCOS (Pivot Data) File; GEO SOFT Affymetrix File Format; GEO SOFT two channel file format; dChip or DFCI core file format; Assignment File Saving System; Special Cases
Appendix: Preferences Files
Appendix: Distance Metrics
Appendix: MeV Script DTD: DTD UML Schema
Appendix: MeV R Integration
Appendix: Bayesian Network & Literature Mining
Appendix: MeV Dependencies
License
Contributors
Out of Memory Errors
Newick tree output
Nexus tree output

Table of Contents

Clustering

Statistics

Classification

Data Reduction

Meta Analysis

Visualization

Miscellaneous

Appendix