- Page 1 and 2: Microarray Data AnalysisUsing BRB-A
- Page 3 and 4: Part I:What is BRB-ArrayTools?3
- Page 5 and 6: Features of BRB-ArrayTools• Capab
- Page 7 and 8: New to ArrayToolsv4.1• Affy ST ar
- Page 9 and 10: Full Installer• Also available is
- Page 11 and 12: Downloading BRB-ArrayTools• After
- Page 13 and 14: Installing BRB-ArrayTools13
- Page 15 and 16: Installing BRB-ArrayTools• Select
- Page 17 and 18: Installing BRB-ArrayTools• Procee
- Page 19 and 20: Installing BRB-ArrayTools• Instal
- Page 21: Excel 2007- loading the add-in• 1
- Page 25 and 26: Expression data(one or more files)E
- Page 27 and 28: Expression data• Input data as ta
- Page 29 and 30: Expression data(one or more files)E
- Page 31 and 32: Gene identifiersTwo examples of a g
- Page 33 and 34: Experiment (Array) descriptors• A
- Page 35 and 36: Expression data(one or more files)E
- Page 37 and 38: Gene listsCancer Genome Anatomy Pro
- Page 39 and 40: Expression data(one or more files)E
- Page 41 and 42: Automatic data importers• General
- Page 43 and 44: Recently Implemented• Can automat
- Page 45 and 46: Pomeroy Dataset• On the Desktop,
- Page 47 and 48: [Hands-on instructions][Importing P
- Page 49 and 50: [Hands-on instructions][Importing P
- Page 51 and 52: [Hands-on instructions][Importing P
- Page 53 and 54: [Hands-on instructions][Importing P
- Page 55 and 56: The collated project workbook• Th
- Page 57 and 58: The collated project workbookExperi
- Page 59 and 60: The collated project workbookFilter
- Page 61 and 62: Part IV:Data filtering andnormaliza
- Page 63 and 64: Data filtering optionsSingle-Channe
- Page 65 and 66: Data filtering optionsData transfor
- Page 67 and 68: Data filtering optionsGene filters:
- Page 69 and 70: Part V:Overview of some analysistoo
- Page 71 and 72: [Optional: Hands-on instructions][S
- Page 73 and 74:
Analysis Wizard• Click on “Arra
- Page 75 and 76:
Finding Genes• Comparing classes
- Page 77 and 78:
Class comparison toolBetween groups
- Page 79 and 80:
Class ComparisonExperimental design
- Page 81 and 82:
Class comparison toolBlocking Facto
- Page 83 and 84:
Class comparison toolRandom varianc
- Page 85 and 86:
Class comparison toolUnivariate sig
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Class comparison toolMultivariate p
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[Hands-on instructions][Class compa
- Page 91 and 92:
Class comparisonSignificance Analys
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Gene set ExpressionComparison• Al
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Efron-Tibshirani's GSA maxmeantest
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[Hands-on instructions][Class Compa
- Page 99 and 100:
Survival analysis tools• Find Gen
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Classification of samples• Cluste
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[Hands-on instructions][Cluster ana
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[Hands-on instructions - cont’d][
- Page 107 and 108:
[Hands-on instructions - cont’d][
- Page 109 and 110:
Cluster reproducibility• Add pert
- Page 111 and 112:
[Hands-on instructions][Multidimens
- Page 113 and 114:
Components of Class Prediction• C
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Gene Selection Criteria115
- Page 117 and 118:
C3. Cross-validating the classifier
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Compound covariate predictor• May
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Linear classifiers for two classes
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Bayesian Compound Covariate• Comp
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Nearest centroid• May be used for
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Class prediction toolClass predicti
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Important notes• Cross validation
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Plug-in utility• A plug-in utilit
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[Additional Plugins]• Class Predi
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Part VI:Independent practice(if tim
- Page 137 and 138:
Acknowledgements• Dr. Richard Sim
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BRB-ArrayToools ListServTo particip
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Exercise SectionUsing the breast tu