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

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Gene lists• Genelists are used for annotation and for defining subsets for analysis. aThese files are located in the ArrayTools installation folder.• Two types of genelists: CGAP, and user-defined• CGAP (Cancer Genome Anatomy Project) genelists are pre-loaded withBRB-ArrayTools.• User-defined genelists are simply text files which the user creates,containing a label specifying the type of identifier, followed by a list ofgene identifiers. The file should be appropriately named to indicateicatewhat type of genes are in the list. Some user-defined genelists areautomatically produced as the result of an analysis, such as classcomparison, class prediction, survival analysis, and hierarchicalclustering of genes.• User-defined genelists are stored in the “project” folder (for projectspecific) or ArrayTools folder (visible to all projects.)36
Gene listsCancer Genome Anatomy Project37
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 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 34 and 35: Experiment descriptorsDescribes the
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 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
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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
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][
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Page 108 and 109:
Page 110 and 111:
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)
Page 128 and 129:
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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