Newport IServer MicroServer iTHX-M User manual

P/N 702083 Rev. 2

Affymetrix GeneChip®Genotyping

Analysis Software Version 4.1 —

User’s Guide

GTYPE Title page.fm Page i Wednesday, August 2, 2006 12:15 PM

For research use only.

Not for use in diagnostic procedures.

Trademarks

Affymetrix®, ®, GeneChip®, HuSNP®, GenFlex®, Flying Objective™,

CustomExpress®, CustomSeq®,NetAffx™, Tools To Take You As Far As Your Vision®,

The Way Ahead™, Powered by Affymetrix™, GeneChip-compatible™, and Command

Console™ are trademarks of Affymetrix, Inc.

All other trademarks are the property of their respective owners.

Limited License Notice

Limited License. Subject to the Affymetrix terms and conditions that govern your use

of Affymetrix products, Affymetrix grants you a non-exclusive, non-transferable,

non-sublicensable license to use this Affymetrix product only in accordance with the

manual and written instructions provided by Affymetrix. You understand and agree

that except as expressly set forth in the Affymetrix terms and conditions, that no

right or license to any patent or other intellectual property owned or licensable by

Affymetrix is conveyed or implied by this Affymetrix product. In particular, no right or

license is conveyed or implied to use this Affymetrix product in combination with a

product not provided, licensed or specifically recommended by Affymetrix for such

use.

Patents

Software products may be covered by one or more of the following patents: U.S.

Patent Nos. 5,733,729; 5,795,716; 5,974,164; 6,066,454; 6,090,555, 6,185,561 6,188,783,

6,223,127; 6,228,593; 6,229,911; 6,242,180; 6,308,170; 6,361,937; 6,420,108; 6,484,183;

6,505,125; 6510,391; 6,532,462; 6,546,340; 6,687,692; 6,607,887; and other U.S. or

foreign patents.

GTYPE Title page.fm Page ii Wednesday, August 2, 2006 12:15 PM

iii

Table of Contents

Introduction 3

ABOUT THIS MANUAL 4

CONVENTIONS USED IN THIS GUIDE 6

ONLINE DOCUMENTATION 8

TECHNICAL SUPPORT 9

CHAPTER 1 GTYPE Overview 13

GTYPE ANALYSIS 13

USING GTYPE WITH GCOS 16

GTYPE WALKTHROUGH 19

MAPPING ANALYSIS WORKFLOW 28

UNIVERSAL TAG WORKFLOW 44

CHAPTER 2 Getting Started 49

OPTIONS FOR USING GTYPE 49

STARTING GTYPE 50

USER INTERFACE COMPONENTS 54

DATA TREE 57

SHORTCUT BAR 72

STATUS LOG 76

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iv Affymetrix GeneChip® Genotyping Analysis Software User’s Guide

CHAPTER 3 Working with Images 79

VIEWING CELL INTENSITY IMAGES 79

ADJUSTING THE IMAGE SETTINGS 84

VIEWING PROBE CELL DATA 89

VIEWING PROBE SET INTENSITY DATA 92

BOOKMARKS 98

DEFAULT IMAGE SETTINGS 101

CHAPTER 4 Analyzing Cell Intensity Data 107

OVERVIEW 107

USING THE ANALYZE DIALOG BOX 110

USING THE DATA TREE 114

USING THE BATCH ANALYSIS WINDOW 117

CHANGING ALGORITHM SETTINGS 128

ANALYSIS DEFAULTS 135

CHAPTER 5 Mapping Analysis Window 139

OVERVIEW 139

FEATURES 140

DISPLAYING RESULTS IN THE MAPPING

ANALYSIS WINDOW 141

GTYPE_manual.book Page iv Wednesday, August 2, 2006 11:31 AM

Contents v

MAPPING ANALYSIS – GENOTYPE CALLS 146

SNP TABLE 149

SCATTER PLOTS 164

CHAPTER 6 Working with Mapping Data 181

SETTING UP SAMPLE ATTRIBUTES 182

IMPORTING PEDIGREE/ATTRIBUTE INFORMATION 185

DISPLAYING DATA IN VIRTUAL ARRAYS 193

CHECKING FOR MENDELIAN INHERITANCE ERROR 201

USING THE SAMPLE MISMATCH REPORT TOOL 208

EXPORTING DATA WITH THE SNP EXPORT TOOL 226

LOSS OF HETEROZYGOSITY ANALYSIS 247

CHAPTER 7 Universal Tag Window 253

OVERVIEW 254

TAG TABLE 256

CHAPTER 8 Probe Intensity Window 263

OVERVIEW 263

INTENSITY PLOT 268

PROBE INTENSITY TABLE 271

DATA DISPLAYED FOR MAPPING ARRAYS 272

GTYPE_manual.book Page v Wednesday, August 2, 2006 11:31 AM

vi Affymetrix GeneChip® Genotyping Analysis Software User’s Guide

CHAPTER 9 NetAffx™Annotations 277

OVERVIEW 277

DOWNLOADING NETAFFX™ANNOTATIONS 279

SELECTING ANNOTATIONS FOR DISPLAY 284

SETTING THE ADVANCED OPTIONS 285

CHAPTER 10 Reports 291

OVERVIEW 292

WORKING WITH REPORTS 299

Appendix A Installing GTYPE Software 307

OVERVIEW 307

REQUIREMENTS 307

INSTALLATION 308

SELECTING A DATABASE 313

INSTALLING GTYPE SERVER COMPONENTS

IN GCOS SERVER 314

Appendix B MPAM Mapping Algorithm 319

THE GENECHIP® 10K MAPPING ARRAY 319

THE MPAM ALGORITHM 321

GTYPE_manual.book Page vi Wednesday, August 2, 2006 11:31 AM

Contents vii

MPAM MAPPING ALGORITHM SETTINGS 331

Appendix C Dynamic Model Mapping Algorithm 337

THE DYNAMIC MODEL MAPPING ARRAY 337

THE DYNAMIC MODEL MAPPING ALGORITHM 339

DYNAMIC MODEL MAPPING ALGORITHM SETTINGS 351

Appendix D Bayesian Robust Linear Model with

Mahalanobis (BRLMM) Distance Classifier

Algorithm 355

INTRODUCTION 356

NORMALIZATION AND ALLELE SUMMARIZATION 359

CLUSTERING SPACE TRANSFORMATION 360

CALLING GENOTYPES 362

ESTIMATING CLUSTER CENTERS AND VARIANCES 363

SPECIAL CASES 367

RESULTS 369

DISCUSSION 370

BRLMM MAPPING ALGORITHM SETTINGS 371

BRLMM RAM REQUIREMENTS 373

REFERENCES 375

GTYPE_manual.book Page vii Wednesday, August 2, 2006 11:31 AM

viii Affymetrix GeneChip® Genotyping Analysis Software User’s Guide

Appendix E Mapping Tool Algorithms 379

SAMPLE MISMATCH ALGORITHM 379

FILTER ALGORITHMS 380

Appendix F IUPAC Base Codes 387

Appendix G File Types 391

Appendix H Working with Windowpanes & Columns 395

Appendix I Hot Key Descriptions 399

Index 403

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Introduction

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GTYPE_manual.book Page 2 Wednesday, August 2, 2006 11:31 AM

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