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Microarray Data AnalysisUsing BRB-A
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Part I:What is BRB-ArrayTools?3
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Features of BRB-ArrayTools• Capab
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New to ArrayToolsv4.1• Affy ST ar
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Full Installer• Also available is
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Downloading BRB-ArrayTools• After
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Installing BRB-ArrayTools13
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Installing BRB-ArrayTools• Select
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Installing BRB-ArrayTools• Procee
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Installing BRB-ArrayTools• Instal
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Excel 2007- loading the add-in• 1
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Part II:Getting your data intoBRB-A
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Expression data(one or more files)E
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Expression dataHorizontally aligned
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Gene identifiers• A gene identifi
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Expression data(one or more files)E
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Experiment descriptorsDescribes the
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Gene lists• Genelists are used fo
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Gene listsUser-defined text files38
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Specify data using thecollate dialo
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Affymetrix CEL file importation•
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Part III:The collated projectworkbo
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[Hands-on instructions][Importing P
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[Hands-on instructions][Importing P
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[Hands-on instructions][Importing P
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• Click “OK”[Hands-on instruc
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Collated project workbookOverview
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Expression data(one or more files)E
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The collated project workbookGene i
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The collated project workbookGene a
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[Hands-on instructions][Data filter
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Data filtering optionsNormalization
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Data filtering optionsGene filters:
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Data filtering optionsGene subsets
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Scatterplot tools• Scatterplot of
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[Optional: Hands-on instructions][S
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Analysis Wizard• Finding GenesFin
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Tools for finding Genes/Genesetscom
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Class Comparison78
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Class comparison tool1. Enter the c
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Average over replicates• If multi
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Find genes lists determined by:84
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[Hands-on instructions][Class compa
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- Page 90 and 91: Gene ontology analysis• In the cl
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- Page 94 and 95: Gene Set ExpressionComparison• Co
- Page 96 and 97: Goeman’s s Global test• Tests t
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- Page 110 and 111: Multidimensional scaling• Rotatin
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- 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
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- Page 126 and 127: Support vector machines(V. Vapnik)
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- Page 132 and 133: Included plugins• Analysis of Var
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- Page 136 and 137: Further help• We hope this class
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