Microarray Data Analysis Using BRB-ArrayTools Version 4.2.0 ...

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[Hands-on instructions ][Class prediction –Pomeroy data]1. Run the Class Prediction tool by clicking on <strong>ArrayTools</strong> Class prediction Class prediction.2. Select the Medulo vs Glio variable as the column defining theclasses. Check the box for using the Random Variance Model.3. Choose the univariate significance alpha=0.001.4. Select Options, check the box for Use separate test set, , andselect the column “TrainingSet”.5. Leave all other options at default levels, and click OK.6. Note the Array Ids which have been misclassified by allmethods.130
Plug-in utility• A plug-in utility now allows users to create their owntools by writing their own scripts written in the Rlanguage• Tools created using the plug-in utility can bedistributed to other users, and added to the Pluginmenu• The user-created plug-ins are stored in the Pluginsfolder of the <strong>ArrayTools</strong> installation folder131
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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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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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• Click “OK”[Hands-on instruc
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Collated project workbookOverview
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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
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 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 132 and 133: Included plugins• Analysis of Var
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Page 136 and 137: 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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Microarray Data Analysis Using BRB-ArrayTools Version 4.2.0 ...

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