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

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Class comparison tool1. Enter the class column from the ‘Experiment descriptor’worksheet that defines the classes for the samples.2. Specify if this is a paired or un-paired analysis. Ananalysis is said to be paired if for example, you have thesame sample from a patient before and after a treatment.You then need a column in the experiment descriptorworksheet that will contain identical values for pair ofarrays.3. If this is an unpaired analysis, do you have a blockingfactor?4. If this is an unpaired analysis, do you have an replicatesyou want to average across?80
Class comparison toolBlocking FactorExperimental designs containing a blocking factor can beperformed by specifying which column in the Experimentdescriptor worksheet contains a blocking variable. Whenselected, the influence of the blocking variable is taken intoconsideration when analyzing the differences between classes.Examples of variables that may be considered as Blockingfactors:‣ Clinical Site for patient data‣ Print set for cDNA spotted arrays‣ Batch of arrays81
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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
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
Page 74 and 75: Analysis Wizard• Finding GenesFin
Page 76 and 77: Tools for finding Genes/Genesetscom
Page 78 and 79: Class Comparison78
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
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[Hands-on instructions ][Class pred
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Included plugins• Analysis of Var
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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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