- 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: Installing BRB-ArrayTools• Procee
- Page 21: Excel 2007- loading the add-in• 1
- Page 24 and 25: Part II:Getting your data intoBRB-A
- Page 26 and 27: Expression data(one or more files)E
- Page 28 and 29: Expression dataHorizontally aligned
- Page 30 and 31: Gene identifiers• A gene identifi
- Page 32 and 33: Expression data(one or more files)E
- Page 34 and 35: Experiment descriptorsDescribes the
- Page 36 and 37: Gene lists• Genelists are used fo
- Page 38 and 39: Gene listsUser-defined text files38
- Page 40 and 41: Specify data using thecollate dialo
- Page 42 and 43: Affymetrix CEL file importation•
- Page 44 and 45: Part III:The collated projectworkbo
- Page 46 and 47: [Hands-on instructions][Importing P
- Page 48 and 49: [Hands-on instructions][Importing P
- Page 50 and 51: [Hands-on instructions][Importing P
- Page 52 and 53: • Click “OK”[Hands-on instruc
- Page 54 and 55: Collated project workbookOverview
- Page 56 and 57: Expression data(one or more files)E
- Page 58 and 59: The collated project workbookGene i
- Page 60 and 61: The collated project workbookGene a
- Page 62 and 63: [Hands-on instructions][Data filter
- Page 64 and 65: Data filtering optionsNormalization
- Page 66 and 67: Data filtering optionsGene filters:
- Page 68 and 69:
Data filtering optionsGene subsets
- Page 70 and 71:
Scatterplot tools• Scatterplot of
- Page 72 and 73:
[Optional: Hands-on instructions][S
- Page 74 and 75:
Analysis Wizard• Finding GenesFin
- Page 76 and 77:
Tools for finding Genes/Genesetscom
- Page 78 and 79:
Class Comparison78
- Page 80 and 81:
Class comparison tool1. Enter the c
- Page 82 and 83:
Average over replicates• If multi
- Page 84 and 85:
Find genes lists determined by:84
- Page 86 and 87:
[Hands-on instructions][Class compa
- Page 88 and 89:
Class comparison toolMultivariate p
- Page 90 and 91:
Gene ontology analysis• In the cl
- Page 92 and 93:
[Hands-on instructions][Significanc
- Page 94 and 95:
Gene Set ExpressionComparison• Co
- Page 96 and 97:
Goeman’s s Global test• Tests t
- Page 98 and 99:
Quantitative trait tool• Selects
- Page 100 and 101:
Survival Gene Set analysis• This
- Page 102 and 103:
Hierarchical clustering tools• Cl
- Page 104 and 105:
[Hands-on instructions - cont’d][
- Page 106 and 107:
[Hands-on instructions - cont’d][
- Page 108 and 109:
[Hands-on instructions - cont’d][
- Page 110 and 111:
Multidimensional scaling• Rotatin
- Page 112 and 113:
Analysis Wizard- Prediction• Clas
- Page 114 and 115:
C1. Gene Selection Criteria• Sele
- Page 116 and 117:
C2. Class prediction Methods• Six
- Page 118 and 119:
Permutation test• Use a permutati
- Page 120 and 121:
Linear classifiers for two classesl
- Page 122 and 123:
Diagonal linear discriminant analys
- Page 124 and 125:
K-nearest neighbor• May be used f
- Page 126 and 127:
Support vector machines(V. Vapnik)
- Page 128 and 129:
Prediction Analysis MicroarrayPAM
- Page 130 and 131:
[Hands-on instructions ][Class pred
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Included plugins• Analysis of Var
- Page 134 and 135:
134
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Further help• We hope this class
- Page 138 and 139:
Technical support• For questions
- Page 140 and 141:
Feedback on this class• Please fi
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