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

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Installing BRB-ArrayTools• After successfully installing BRB-ArrayTools, you will beprompted with the message below.• Click “OK” as the software has been installed as an add-in toExcel.20
Excel 2007- loading the add-in• 1:Click on the Microsoft ‘Office’ button on the top left corner of the Excel menu.• 2. Then, select the “Excel Options” button on the bottom right.• 3: Click on “Trust Center”• 4. Then click on “Trust Center Settings”• 5: Choose the “Macro Settings” from the left hand panel.• 6. Check “Enable all macros” and “Trust access to VBA project.”• 7. Click the “OK” button.• 8: Choose the “Add-ins” option from the left hand tab.• 9. Click “BRB-ArrayTools” on the Active or Inactive application add-in.• 10. Hit the “Go” button down at the bottom.• 11. Check all the three “Add-ins”,, BRB-ArrayToolsArrayTools, RServer and CGHTools.• 12. Then click OK.• If you don’t t see the “Add-ins” ribbon along side “Home Insert…Review View” panelat the top then please close Excel and re-start.• On clicking on Add-Ins tab, all the three Add-Ins should be listed there namely:ArrayTools, CGHTools and RServer add-ins.21
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: Installing BRB-ArrayTools• Instal
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 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 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 106 and 107:
Page 108 and 109:
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
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
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Microarray Data Analysis Using BRB-ArrayTools Version 4.2.0 ...

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