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MeV Manual 4.0

MeV Manual 4.0

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Published by: Ponlapat Yonglitthipagon on Dec 03, 2012
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02/27/2014

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MeV
MultiExperiment Viewer
Version 4.0July 06, 2006
 
 2
Table of Contents
 
General Information...............................................................6
 
TM4 Software Overview........................................................7
 
Starting MultiExperiment Viewer........................................8
 
Loading Expression Data.......................................................9
 
 Loading MeV (.mev) Format Files......................................................................9
 
 Loading TIGR Array Viewer (.tav) Files..........................................................10
 
 
 Loading Affymetrix Data (.txt, .TXT) Files.......................................................12
 
 Loading GenePix (.gpr) Data Files..................................................................13
 
 Loading Agilent Files........................................................................................14
 
 
 Result Navigation Tree.................................................................................21
 
The History Node and Log............................................................................21
 
Adjusting the Data................................................................23
 
 Adjustment / Filter Overview............................................................................23
 
 Replicate Analysis.............................................................................................24
 
 Data Transformations.......................................................................................25
 
 
 Data Source Selection.......................................................................................32
 
Display Options.....................................................................34
 
Sample Annotation............................................................................................34
 
Selecting Gene Annotation................................................................................36 
 
Color Scheme Selection....................................................................................36 
 
Setting Color Scale Limits................................................................................37 
 
 Element Appearance.........................................................................................39
 
Viewer Descriptions..............................................................40
 
Overview...........................................................................................................40
 
 Expression Images............................................................................................40
 
 Expression Graphs............................................................................................43
 
Centroid Graphs...............................................................................................45
 
 
 3
Table Views.......................................................................................................47 
 
Common Viewer Activities................................................................................49
 
Working with Clusters.........................................................51
 
Storing Clusters and Using the Cluster Manager............................................51
 
Utilities Menu........................................................................58
 
Creating Output....................................................................63
 
Saving the Analysis.......................................................................................63
 
Saving the Expression Matrix.......................................................................63
 
Saving Viewer Images...................................................................................64
 
Saving Cluster Data......................................................................................64
 
Modules..................................................................................65
 
 Description Conventions and General Pointers...........................................................65
 
 HCL: Hierarchical clustering.......................................................................67 
 
TEASE: Tree-EASE.......................................................................................72
 
ST: Support Trees.........................................................................................78 
 
SOTA: Self Organizing Tree Algorithm........................................................81
 
 RN: Relevance Networks...............................................................................86 
 
KMC: K-Means/K-Medians Clustering........................................................89
 
KMS: K-Means / K-Medians Support...........................................................91
 
CAST: Clustering Affinity Search Technique...............................................93
 
QTC: QT CLUST..........................................................................................95
 
SOM: Self Organizing Maps.........................................................................97 
 
GSH: Gene Shaving....................................................................................100
 
FOM: Figures of Merit...............................................................................102
 
PTM: Template Matching...........................................................................106 
 
TTEST: T-tests............................................................................................109
 
SAM: Significance Analysis of Microarrays...............................................117 
 
 ANOVA: Analysis of Variance....................................................................121
 
TFA: Two-factor ANOVA...........................................................................124
 
SVM: Support Vector Machines..................................................................126 
 
KNNC: K-Nearest-Neighbor Classification...............................................133
 
 DAM: Discriminant Analysis Module.........................................................137 
 
 LEM: Linear Expression Maps...................................................................142
 

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