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

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BRB-ArrayToolsAn Integrated Software Tool forDNA Microarray Analysis• Developed under the direction of Dr. Richard Simon of theBiometrics Research Branch, NCI.• Software was developed with the purpose of deployingpowerful statistical tools for use by biologists.• Analyses are launched from user-friendly Excel interface.Also requires installation of a free software called R forrunning back-end programs. Current requirement for R is v2.12.0. Publicly available from BRB website:http://linus.nci.nih.gov/BRB-ArrayTools.html4
Features of BRB-ArrayTools• Capability to collate (sort into an expression data matrix) microarray datafrom a set of experiments, and apply filtering and normalization.Compute RMA/GC-RMA/MAS5.0 RMA/MAS5.0 probeset summaries andnormalization. BRB-ArrayTools was designed to analyze a set of arraysrather than a single array.• The focus of the software has been the implementation of statisticalicalmethodology which utilizes the sample descriptors (supervised analysis).alysis).• Scatterplots, hierarchical clustering, and multidimensional scaling analysesalso provide powerful visualization tools.• Gene annotations are integrated into analysis output to inform the tanalysis results. Also, includes analyses using Biocarta,KEGG andBroad/MIT pathways.• Advanced users may program their own plugin analysis tools within n BRB-ArrayTools.5
Page 1 and 2: Microarray Data AnalysisUsing BRB-A
Page 3: Part I:What is BRB-ArrayTools?3
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 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 52 and 53: • 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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Class comparison toolMultivariate p
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Gene ontology analysis• In the cl
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[Hands-on instructions][Significanc
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Gene Set ExpressionComparison• Co
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Goeman’s s Global test• Tests t
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Quantitative trait tool• Selects
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Survival Gene Set analysis• This
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Hierarchical clustering tools• Cl
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[Hands-on instructions - cont’d][
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Multidimensional scaling• Rotatin
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Analysis Wizard- Prediction• Clas
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C1. Gene Selection Criteria• Sele
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C2. Class prediction Methods• Six
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Permutation test• Use a permutati
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Linear classifiers for two classesl
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Diagonal linear discriminant analys
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K-nearest neighbor• May be used f
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Support vector machines(V. Vapnik)
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Prediction Analysis MicroarrayPAM
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[Hands-on instructions ][Class pred
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Included plugins• Analysis of Var
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134
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Further help• We hope this class
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Technical support• For questions
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Feedback on this class• Please fi
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Microarray Data Analysis Using BRB-ArrayTools Version 4.2.0 ...

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