Newport iServer MicroServer iTHX-M Operator's Manual

Affymetrix GeneChip® Genotyping Analysis Software Version 4.1 — User’s Guide all-guides.co m ...

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 ...

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 I ...

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 ...

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 ...

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 30 ...

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 SU ...

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 ...