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

More documents

Recommendations

Info

Diagonal linear discriminant analysis• May be used for classifying among two or moreclass labels• Use F-test Fto screen for genes which areunivariately significant in classifying the samples• Seeks a linear combination of the variables whichhas a maximal ratio of the separation of the classmeans to the within-class variance, where genes areassumed to be uncorrelated122
Bayesian Compound Covariate• Compound Covariate score is computed for allthe samples in the cross-validated training set.• The CCP-scores of samples in each class of thetraining set are assumed to be from a Gaussiandistribution.• If prior probabilities are ½ - the BCCP issimilar to the CCP.123
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 32 and 33:
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 48 and 49:
Page 50 and 51:
Page 52 and 53:
• Click “OK”[Hands-on instruc
Page 54 and 55:
Collated project workbookOverview
Page 56 and 57:
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
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 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
Page 130 and 131: [Hands-on instructions ][Class pred
Page 132 and 133: Included plugins• Analysis of Var
Page 134 and 135: 134
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
show all

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

Create successful ePaper yourself

Delete template?

Save as template?