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

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Support vector machines(V. Vapnik)• Implemented only for classifying among twoclass labels• Select genes which univariately classify thesamples• The SVM predictor is implemented as a linearfunction of the log-ratios or the log-intensitiesover the significant genes, that best separatesthe data subject to penalty costs on the numberof specimens misclassified.126
Class prediction toolClass prediction vs. binary tree prediction• The class prediction tool has more options: may select allprediction methods simultaneously, may use pairedsamples, may use randomized variance option.• The binary tree prediction tool splits the classes intogroups of subclasses. At each node in the tree, the binarytree prediction tool decides how to split the classes intotwo groups based on either a leave-oneone-out out or a K-fold Kcross-validation. The binary tree prediction tool may beuseful if there is a hierarchical structure to the classes.• However, the binary tree prediction may be very slow for alarge number of samples. Therefore, a K-fold Kcross-validation should be used if the number of samples islarge.• Currently the tool is limited to five classes, and requires atleast four samples per class for good prediction.127
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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
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
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 128 and 129: Prediction Analysis MicroarrayPAM
Page 130 and 131: [Hands-on instructions ][Class pred
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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