Newport iServer MicroServer iTHX-M User manual

P/N 702083 Rev. 2
Affymetrix GeneChip®Genotyping
Analysis Software Version 4.1 —
User’s Guide
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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.
Copyright
©2006 Affymetrix, Inc. All rights reserved.
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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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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
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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
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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
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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
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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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Introduction
Welcome to the Affymetrix GeneChip®Genotyping Analysis
Software (GTYPE) User’s Guide. The GTYPE 4.1 software
(PN 690051) is part of the GeneChip®mapping array system,
specifically designed to give highly accurate, automated, SNP allele
calls for the GeneChip®mapping arrays. In addition, GTYPE was
developed to enable workflows for a variety of SNP mapping
applications.
GTYPE is an evolution from GDAS 3.0 (GeneChip®DNA Analysis
Software) and builds on the high-quality genotyping, quality control
reporting and streamlined data analysis in GDAS 3.0. With the
launch of the Mapping 500K Array Set, researchers are now able to
perform large scale association studies. In anticipation of increased
sample sizes for larger projects and increased file sizes for 500K
analysis, GTYPE 4.1 enhancements are designed to streamline data
analysis for projects with thousands of samples.
GTYPE Benefits include:
• Automatic SNP allele calling with quality scores for Mapping
10K, 100K and 500K Array Sets
• High allele calling accuracy and reproducibility
• Detection of rare alleles
• Batch import for sample annotation, gender identification, and
Mendel-error checking
• Batch export into tab-delimited, GeneHunter open source
software, Haploview, and MERLIN compatible formats
• Advanced SNP filtering by Allele Frequency, Hardy-Weinberg
Equilibrium, Mendelian-error, and SNP call rate
• Analysis of built-in shared SNPs on the100K and 500K array sets
Directions for installing GTYPE are in Appendix A, Installing GTYPE
Software, on page 307.
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4Affymetrix GeneChip® Genotyping Analysis Software User’s Guide
• A Virtual Array feature, which allows the 100K Array Set and/or
500K Array Set to be managed as a single-array data set
• The FileSets feature, which allows customized groupings of
samples from multiple projects
About this Manual
This manual presents information about the GTYPE software in the
following chapters and appendices:
•Chapter 1, GTYPE Overview: Introduces the GTYPE software,
with walk-throughs showing different operations.
•Chapter 2, Getting Started: Describes the options for using
GTYPE, how to start GTYPE, and the interface components.
•Chapter 3, Working with Images: Describes how to view the cell
intensity data in the Image window.
•Chapter 4, Analyzing Cell Intensity Data: Describes how to analyze
cell intensity data for Mapping and GenFlex®Tag assays.
•Chapter 5, Mapping Analysis Window: Describes the analysis
window that displays results for MPAM, DM, and BRLMM
mapping array analysis.
•Chapter 6, Working with Mapping Data: Describes the tools for
working with MPAM, DM, and BRLMM mapping algorithm
analysis results.
•Chapter 7, Universal Tag Window: Describes the display of analysis
results for GenFlex®Tag assays.
•Chapter 8, Probe Intensity Window: Describes how to view the probe
intensity values for particular probe sets for mapping assays.
•Chapter 9, NetAffx™Annotations: Describes how to select and
download NetAffx annotations for the mapping analysis results.
•Chapter 10, Reports: Describes how to generate and view reports
for the analyses performed in GTYPE.
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Welcome 5
The appendices include additional information and reference
information:
•Appendix A, Installing GTYPE Software: Provides installation
instructions and information on initializing GTYPE.
•Appendix B, MPAM Mapping Algorithm: Describes the Modified
Partitioning Around Medoids (MPAM) mapping algorithm and
the user-definable parameters.
•Appendix C, Dynamic Model Mapping Algorithm: Describes the
Dynamic Model (DM) mapping algorithm and the user-definable
parameters.
•Appendix D, Bayesian Robust Linear Model with Mahalanobis
(BRLMM) Distance Classifier Algorithm: Describes the BRLMM
mapping algorithm and the user-definable parameters.
•Appendix E, Mapping Tool Algorithms: Describes the algorithms
used by the Mapping Tools.
•Appendix F, IUPAC Base Codes: Lists the IUPAC base codes used
by GTYPE.
•Appendix G, File Types: Describes the file types used by GTYPE.
•Appendix H, Working with Windowpanes & Columns: Describes how
to resize windowpanes and resize or hide table columns.
•Appendix I, Hot Key Descriptions: Lists hotkeys used by GTYPE.
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6Affymetrix GeneChip® Genotyping Analysis Software User’s Guide
Conventions Used in This Guide
This manual provides a detailed outline for all tasks associated with
Affymetrix®GTYPE software. Various conventions are used
throughout the manual to help illustrate the procedures described.
Explanations of these conventions are provided below.
STEPS
Instructions for procedures are written in a numbered step format.
Immediately following the step number is the action to be performed.
Following the response, additional information pertaining to the step
may be found and is presented in paragraph format. For example:
1. Click Yes to continue.
The Delete task proceeds.
In the lower right pane the status is displayed.
To view more information pertaining to the delete task, right-click
Delete and select View Task Log from the shortcut menu.
FONT STYLES
Bold fonts indicate names of commands, buttons, options or titles
within a dialog box. When asked to enter specific information, the
input opens in italics within the procedure being outlined.
For example:
1. Click the Find toolbar button ; or
Select Edit Find from the menu bar.
The Find dialog box opens.
2. Enter AFFX-BioB-5_at in the Find what box, then click Find
Next to view the first search result.
3. Continue to click Find Next to view each successive search result.
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Welcome 7
SCREEN CAPTURES
The steps outlining procedures are frequently supplemented with
screen captures to further illustrate the instructions given.
ADDITIONAL COMMENTS
Throughout the manual, text and procedures are occasionally
accompanied by special notes. These additional comments and their
meanings are described below.
The screen captures depicted in this manual may not exactly match
the windows displayed on your screen.
Information presented in Tips provide helpful advice or shortcuts
for completing a task.
The Note format presents supplemental information pertaining to
the text or procedure being outlined.
The Important format presents important information that may
affect the accuracy of your results.
Caution notes advise you that the consequence(s) of an action may
be irreversible and/or result in lost data.
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8Affymetrix GeneChip® Genotyping Analysis Software User’s Guide
Online Documentation
The CD with the GTYPE software includes an electronic version of
this guide. The electronic version is in Adobe Acrobat format (a *.pdf
file) and is readable with the Adobe Acrobat Reader software, available
at no charge from Adobe at http://www.adobe.com.
The GTYPE software includes on-line help.
To access the on-line help:
• Click the Help button in the main toolbar, or select Help
Contents from the main menu.
Warnings alert you to situations where physical harm to person or
damage to hardware is possible.
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Welcome 9
Technical Support
Affymetrix provides technical support to all licensed users via phone or
E-mail. To contact Affymetrix®Technical Support:
AFFYMETRIX, INC.
3420 Central Expressway
Santa Clara, CA 95051 USA
Tel: [phone] (1-888-DNA-CHIP)
Fax: [phone]
[e-mail]
[e-mail]
AFFYMETRIX UK Ltd.,
Voyager, Mercury Park,
Wycombe Lane, Wooburn Green,
High Wycombe HP10 0HH
United Kingdom
UK and Others Tel: [phone]
France Tel: [phone]
Germany Tel: [phone]
Fax: [phone]
[e-mail]
[e-mail]
Affymetrix Japan K.K.
Mita NN Bldg. 16F
4-1-23 Shiba Minato-ku,
Tokyo 108-0014 Japan
Tel. [phone]
Fax: [phone]
[e-mail]
[e-mail]
www.affymetrix.com
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10 Affymetrix GeneChip® Genotyping Analysis Software User’s Guide
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Chapter 1GTYPE Overview
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Chapter 1
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