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

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Limitations of BRB-ArrayTools• Available only on the PC. As well as on an Apple macbookpro machine with Windows OS installed with Apple’sbootcamp software• Currently compatible with MS Vista/ Windows 7 and Excel2007/ 2010 .• Also works on a 64- bit machine with Windows OS.• Importation of Affymetrix CEL files using RMA/GC-RMA method requires a large memory capacity even forrelatively large sets of arrays and may further limit thenumber of arrays which can be imported.6
New to ArrayToolsv4.1• Affy ST array importer.• Enhanced visualizations and interactive plots.• Enhanced the Heatmap in clustering.• New plug-ins:Adaboost and Lassoed PC.• A new gene filtering to handle redundant probe setsthat correspond to the same gene.• Utility: To obtain drug information based on a genelist.• Ability to import custom expression arrays andannotations by using the gene identifiers.7
Page 1 and 2: Microarray Data AnalysisUsing BRB-A
Page 3 and 4: Part I:What is BRB-ArrayTools?3
Page 5: Features of BRB-ArrayTools• Capab
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
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
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Analysis Wizard• Finding GenesFin
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Tools for finding Genes/Genesetscom
Page 78 and 79:
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
Page 98 and 99:
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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Page 108 and 109:
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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
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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