UserGuide

Affymetrix® Molecular Diagnostic

Software
Operating System Software for
GeneChip® System 3000Dx v.2

IVD For In Vitro Diagnostic Use.

REF P/N 703230 Rev. 2

 2

Trademarks
Affymetrix®, CytoScan®, and GeneChip® are registered trademarks of Affymetrix, Inc. All other trademarks are the property of their
respective owners.

Limited License
Affymetrix hereby grants to buyer a non-exclusive, non-transferable, non-sublicensable license to Affymetrix’ Core Product IP to use the
product(s), but only in accordance with the product labels, inserts, manuals and written instructions provided by Affymetrix. “Core Product
IP” is the intellectual property owned or controlled by Affymetrix as of the shipment date of a product that covers one or more features of
the product that are applicable in all applications of the product that are in accordance with the product labels, inserts, manuals and written
instructions provided by Affymetrix. The license granted herein to buyer to the Core Product IP expressly excludes any use that: (i) is not in
accordance with the product labels, inserts, manuals and written instructions provided by Affymetrix, (ii) requires a license to intellectual
property that covers one or more features of a product that are only applicable within particular fields of use or specific applications, (iii)
involves reverse engineering, disassembly, or unauthorized analysis of the product and/or its methods of use, or (iv) involves the re-use of a
consumable product. Buyer understands and agrees that except as expressly set forth, no right or license to any patent or other intellectual
property owned or controlled by Affymetrix is granted upon purchase of any product, whether by implication, estoppel or otherwise. In
particular, no right or license is conveyed or implied to use any product provided hereunder in combination with a product or service not
provided, licensed or specifically recommended by Affymetrix for such use. Furthermore, buyer understands and agrees that buyer is solely
responsible for determining whether buyer possesses all intellectual property rights that may be necessary for buyer’s specific use of the
product, including any rights from third parties.

Patents
Array Software: Products may be covered by one or more of the following patents: U.S. Patent Nos. 5,733,729; 5,795,716; 6,066,454;
6,090,555; 6,185,561; 6,188,783; 6,223,127; 6,228,593; 6,229,911; 6,308,170; 6,361,937; 6,420,108; 6,484,183; 6,505,125; 6,510,391; 6,532,462;
6,546,340; 6,567,540; 6,584,410; 6,611,767; 6,687,692; 6,826,296; 6,882,742; 6,957,149; 6,965,704; 6,996,475; 7,068,830; 7,130,458; 7,215,804;
7,424,368; 7,634,363; 7,822,555; 7,991,564; 7,992,098; 8,190,373; 8,498,825 and other U.S. and foreign patents.

Manufacturer

Affymetrix Inc.
3420 Central Expressway
Santa Clara, CA 95051 USA

Copyright
©2014-2015 Affymetrix, Inc. All rights reserved.

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Contents

Chapter 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Indications for Use . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Other Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Context-Sensitive Help . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Complete Help System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Terminology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Text Alerts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Technical Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
European Representative . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

Chapter 2 System Overview. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

Hardware . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Standard Hardware Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Optional Hardware Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Optional Hybridization Oven . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
AMDS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
ASM . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
AMDS User Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Workflow Pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Administrator Pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
User and System Information Panes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

Chapter 3 System Operation Basics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

Before you Begin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Start and Shut Down the System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Start the Workstation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Log onto AMDS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Start the Fluidics Station and Scanner . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Log Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Shut Down . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Change Password . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Use of the Barcode Reader . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Edit Multiple Fields in AMDS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Contiguous Select and Enter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Non-Contiguous Select and Enter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
How to Hold Array Cartridges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
E-Signatures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

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 Contents 4

Chapter 4 Running Test Requests . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24

Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Before you Begin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Working with Test Requests . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Active Worklist . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Enter a Test Request . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Delete a Test Request . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Edit a Test Request . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Batch Edit a Test Request . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Add Information to a Test Request . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
View Assay Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
Cancel a Test Request . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
Register a Test Request . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
Associate Test Requests, Arrays, and Reagent Kit IDs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Troubleshooting Registration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
Oven Hybridization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
Set Up Oven Hybridization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
Start and Monitor Hybridization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
End Hybridization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Hybridization Errors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Wash and Stain Arrays in the Fluidics Station 450Dx v.2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Preparation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Associate Test Requests . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Start Fluidics Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Scanner 3000Dx v.2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Normal Operational Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Manual Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
Stop a Scanner Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
Data Processing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Review Test Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Non-Active Worklist . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39

Chapter 5 Troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
Types of Errors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
Instrument Errors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
Test Request Errors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
Operational Errors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Resolving Alerts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Instrument Troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
Scanner Status Error . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44

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 Contents 5

Appendix A AMDS Administrative Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47

View Logs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
System Logs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Audit Logs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
Export and Burn Log Files to CD or DVD . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
Manage Assays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
Install an Assay . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
Deactivate an Assay . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
Repair or Reactivate an Assay . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
Install a Server Certificate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
Manage Users . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
AMDS User Roles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
Add a User . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
Edit a User . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
Manage the System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
Change System Management Windows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
Manage Instrument Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
View User Performed Service Logs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Archive and Purge Test Requests . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Set General Configurations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64

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Chapter 1
Introduction

This User Guide gives detailed information for use of the Affymetrix® Molecular Diagnostic Software
(AMDS) and an overview of the operation of the GeneChip® System 3000Dx v.2 (GCS 3000Dx v.2).

In this chapter:
 Indications for Use

 Other Documentation

 Context-Sensitive Help

 Complete Help System

 Terminology

 Text Alerts

 Technical Support

 European Representative

Indications for Use

GCS 3000Dx v.2 is intended to measure fluorescence signals of labeled DNA and RNA targets
hybridized to Affymetrix arrays.

Other Documentation
 GeneChip® System 3000Dx v.2 User Guide
 Affymetrix® Molecular Diagnostic Software (AMDS) Quick Reference Card
 Tooltip help1
 Online Help2

Context-Sensitive Help
AMDS is the operating software for the GCS 3000Dx v.2. The AMDS online help system provides
content-sensitive help.
1. Click Help.
2. Use the question mark cursor to click on parts of the window.
The help topic associated with the selected area is shown in the lower half of the center panel and
includes information about the:
 Workflow Pane
 Administrator Pane
 User Details Pane
 Device Status Pane
 Alerts and Alert Details Panes

1 To use this feature, place mouse cursor over an interface component to view its description or un-truncate truncated data.
2 To access, click:

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 Chapter 1 | Introduction 7

Complete Help System

To view:
1. Click Help
2. Click anywhere on the AMDS interface.
3. On the Help toolbar, click Show Navigation (Figure 1.1) to see the complete help system.

Figure 1.1 Show Navigation Button on Help tool bar

4. Use the navigation buttons to search for and select help topics.

Terminology
 Test Request—Unique record of an assay performed on a specimen. Repeated runs of the same
specimen are represented by multiple test requests. Each test request is associated with a specific array
cartridge.
 Assay Software Module (ASM)—The software package that runs an assay. ASMs are supplied by
Affymetrix or authorized partners in the form of a CD.
 Assay—Procedure that processes the specimen to produce a result, includes bench work and running
through the GCS3000Dx v2 workflow. In this manual, assay refers to the ASM.
 Array—A microarray is a glass substrate with oligonucleotide probes. A plastic cartridge surrounds and
protects the array and forms the array cartridge (see Figure 1.1). Array also typically refers to the array
cartridge.
 Fluidics station or FS450Dx–GeneChip® Fluidics Station 450Dx v.2
 Scanner–GeneChip® Scanner 3000Dx v.2 with AutoLoaderDx v.2

Text Alerts
Text alerts draw your attention to a particular piece of information. There are five types of text alerts:
Note, Important, Caution, Warning, and Danger.

NOTE: Information that may be of interest or of help to a user but is not critical to the primary
purpose of the text.

IMPORTANT: Information that is essential to the successful use of a product or the

completion of a procedure and is not safety related.

CAUTION: An alert to the user of hazards that, if not avoided, can cause minor or moderate
personal bodily injury and/or damage to an instrument or loss of data.

WARNING: Alerts the user to hazards that, if not avoided, can cause serious bodily injury or
death, or produce potentially incorrect data that could cause harm to a patient.

DANGER: Dangers alert the user to an imminent hazard that, if not avoided, will cause
serious bodily injury or death, or will produce a result that could cause serious harm to a
patient.

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 Chapter 1 | Introduction 8

Technical Support
Consult this user manual and online help and review the troubleshooting sections before you contact
Affymetrix technical support for unresolved issues. For complete contact information and specific
regional support contact information, go to www.affymetrix.com/browse/contactUs.jsp.

Affymetrix, Inc.
3420 Central Expressway
Santa Clara, CA 95051
USA
www.affymetrix.com

Email: support@affymetrix.com
Tel: 1-888-362-2447 (1-888-DNA-CHIP)
Fax: 1-408-731-5441

Affymetrix UK Ltd.
Voyager, Mercury Park,
Wycombe Lane, Wooburn Green,
High Wycombe HP10 0HH
United Kingdom Tel: +44 (0) 1628 552550
Fax: +44 (0) 1628 552585
France Tel. +33 08-00-91-95-05
Germany Tel. +49 01803-001334
Italy Tel. +39 800-91-59-74
Email: supporteurope@affymetrix.com

Affymetrix Japan, K.K.

ORIX Hamamatsucho Bldg. 7F
1-24-8 Hamamatsucho, Minato-ku
Tokyo 105-0013, Japan
Tel: +81 3-6430-4030
Fax: +81 3-6430-4021
Email: supportjapan@affymetrix.com

European Representative

Emergo Europe
Molenstraat 15
2513 BH, The Hague
The Netherlands

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 Chapter 1 | Introduction 9

Quick Reference Card Ordering Information

Table 1.1

Item Part Number

Affymetrix Molecular Diagnostic Software English—08-0262

(AMDS) Quick Reference Card Chinese—08-0262 CN
Danish—08-0262 DA
German—08-0262 DE
Spanish—08-0262 ES
French—08-0262 FR
Greek—08-0262 GR
Italian—08-0262 IT
Japanese—08-0262 JP
Dutch—08-0262 NL
Portuguese—08-0262 PT
Swedish—08-0262 SE

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Chapter 2
System Overview

The GeneChip® System 3000Dx v.2 (GCS 3000Dx v.2) consists of hardware and software components
for processing microarrays based on assay parameters.The Affymetrix® Molecular Diagnostic Software
(AMDS) manages assay workflows.

In this chapter:
 Hardware

 Software

 AMDS User Interface

Hardware

Standard Hardware Components

The GCS 3000Dx v.2 comes with these standard hardware components:
 System Workstation

 GeneChip® Fluidics Station 450Dx v.2

 GeneChip® Scanner 3000Dx v.2 with AutoLoaderDx v.2

 Barcode Reader

 Hardware Firewall

System Workstation, Monitor, and Soundbar

Figure 2.1 System Workstation

AMDS is loaded on the workstation (Figure 2.1). It provides the hardware interface to other system
components. Because the workstation is a dedicated system, it is locked down to prevent other uses. A
monitor and soundbar (not pictured) are part of the workstation system.

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 Chapter 2 | System Overview 11

Fluidics Station 450Dx v.2

Figure 2.2 Fluidics Station 450Dx v.2

The Fluidics Station (Figure 2.2) consists of four modules installed in a single housing. Each module
holds a single array and performs the washing and staining functions for that array. Up to 8 stations can
communicate with one system workstation.
Each module controls the addition of target and staining fluids to the array cartridge and array washing.
Each module contains a pump, valve, thermo-electric system, and LCD that are controlled by scripts
provided in the Assay Software Module (ASM). These scripts are automatically downloaded to each
module and stored in its electronic memory.

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Scanner 3000Dx v.2 with AutoLoaderDx v.2

Figure 2.3 Scanner 3000Dx v.2 with AutoLoaderDx v.2

The Scanner 3000Dx v.2 with AutoLoaderDx v.2 (Figure 2.3) is a wide-field, epifluorescent, confocal,
scanning laser microscope.It scans the chip after staining on the Fluidics Station. Array cartridges are
loaded into the scanner by the AutoLoaderDx v.2 (an automatic handler) before scanning and returned
to the AutoLoaderDx v.2 when scanning finishes.

Barcode Reader

Figure 2.4 Barcode Reader

The barcode reader (Figure 2.4) is used to enter barcode-encoded information from:
 Array cartridge

 Fluidics station

 Specimen identification

 Reagent lot number

 Other identification information

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 Chapter 2 | System Overview 13

Hardware Firewall

Figure 2.5 Hardware Firewall

The hardware firewall (Figure 2.5) protects against unauthorized access to the workstation. It is a
required component of the system.

Optional Hardware Components

Additional components are:
 Uninterruptible power supply (UPS)–must meet Affymetrix specifications

 Printer–must meet Affymetrix specifications

Contact Affymetrix for optional hardware component specifications.

Optional Hybridization Oven

Depending on the type of assay, you may need a hybridization oven to prepare arrays for testing.
Requirements for a hybridization oven that connects to AMDS are:

Table 2.1

Input Voltage 100–120 VAC, 5 A maximum or 220–240 VAC, 2.5 A maximum

50–60 Hz

Rotisserie Rotation Speed 10–80 RPM, programmable to 1 RPM

Oven Temperature Set Point 30–70°C, programmable to 0.1°C

Programmable Range

Time to Temperature 30 minutes from ambient to 60°C

Oven Temperature Accuracy 1.0°C from 35–60°C

Communications Nine-pin RS-232 port, 9600 Baud rate

Monitors and reports oven temperature, rotisserie rotation rate, and oven status

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 Chapter 2 | System Overview 14

Requirements for a hybridization oven that does not connect to AMDS are:

Table 2.2

Input Voltage 100–120 VAC, 5 A maximum or 220–240 VAC, 2.5 A maximum

50–60 Hz

Rotisserie Rotation Speed 10–80 RPM, programmable to 1 RPM

Oven Temperature Set Point 30–70°C, programmable to 0.1°C

Programmable Range

Time to Temperature 30 minutes from ambient to 60°C

Oven Temperature Accuracy 1.0°C from 35–60°C

Communications NA

Software
There are two types of software:
 Affymetrix ® Molecular Diagnostic Software (AMDS)

 Assay Software Modules (ASM)

AMDS
AMDS is the user interface for the system. It provides control of the instruments, assay workflow, and
the data collection and management processes. When array scanning finishes, data is passed through
AMDS to the ASM. Alternatively, AMDS transfers the data to a network location for downstream
analysis. AMDS also assists you in installing and deactivating an ASM.
AMDS tools:
 Control assay workflows and show test results

 Perform administrative functions

 Troubleshoot the system

ASM
ASMs provide the necessary parameters for processing an array through its entire workflow. ASMs
contain the algorithms and reporting functions to produce the result specific to that ASM. ASM user
manuals give detailed instructions that are unique to specific assays.

NOTE: For ASMs that allow auto-transfer of data, AMDS auto-transfers data (including DAT
and CEL files) to your network where it is available for downstream analysis. Your network
location must have ample storage and the correct access permissions for this auto-transfer
feature to work.

AMDS User Interface

The AMDS user interface consists of three sections (Figure 2.6):
 Left Panel–Workflow and Administration panes

 Center Panel–Gives information based on your selection in the left pane; also shows online help when
selected
 Right Panel–User Details, Device Status, Alert, and Alert Details panes

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 Chapter 2 | System Overview 15

Figure 2.6 AMDS User Interface

Center Panel

Left Panel Right Panel

Workflow Pane
Buttons are:
 Active Worklist

 Registration

 Hybridization Oven

 Fluidics

 Scanner

 Non-Active Worklist

When you select an item, the associated worklist opens in the center panel. A blue arrow next to the
selected item shows that it has been selected.

Active Worklist
A test request is active until processing finishes or it is canceled. While a test request is active, you can
view its status by clicking Active Worklist. Data associated with a test request appear only on the Active
Worklist and the current workflow stage of the test request. Active Worklist enables you to:
 View the current status of all active test requests

 Create new test requests

 View and approve test results

You cannot edit information in the Active Worklist. This worklist is maintained and updated by AMDS.

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 Chapter 2 | System Overview 16

Registration Worklist
The Registration Worklist is the next step in the workflow. This step allows you to associate a test request
with an array cartridge and adds the target preparation reagent kit lot numbers (if these are supported by
the ASM).

Hybridization Oven Worklist

The Hybridization Worklist step allows you to enter oven hybridization data and processes the array in
the hybridization oven.
Some assays do not use a hybridization oven. Instead, they perform hybridization on the fluidics station.
Test requests that are associated with these assays skip this step and proceed to fluidics.

Fluidics Worklist
The Fluidics step allows you to associate a test request with a fluidics station and module and runs the
associated fluidics script. The selected station and module wash and stain the array.

Scanner Worklist
The Scanner selection opens the Scanner Worklist. AMDS automates control of the scanner and uses
the assay information provided by the ASM to manage the scanner settings for each type of array. After
scanning, AMDS automatically grids the image, computes intensities, and either runs an ASM-specific
analysis algorithm to generate a result or transfers the files to data storage.

Non-Active Worklist
The Non-Active Worklist selection shows non-active test requests. The system moves test requests to
the Non-Active Worklist when processing in AMDS finishes.

Administrator Pane
The Administrator Pane (Figure 2.7) is below the Workflow Pane. It is visible to everyone, but only
Laboratory Supervisors and System Maintainers use it.

Figure 2.7 The Administrator Pane

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 Chapter 2 | System Overview 17

User and System Information Panes

The right panel of the user interface has four panes that give up-to-date user details and device status.

User Details Pane

The User Details pane (Figure 2.8) is in the top portion of the right panel. Here you can:
 Log off

 See who is logged in and their role

 See system time and date

 Change passwords

 Shut down the system

Figure 2.8 User Details Pane

Device Status Pane

The Device Status pane is just below the User Details pane (Figure 2.9).

Figure 2.9 Device Status Pane

This pane is an instrument status dashboard, providing color-coded status for each system device.
 Green–Device is operating normally

 Yellow–Abnormal condition detected

 Red–Communications issue or a device failure

AMDS provides status for the fluidics station, scanner, and printer, and for hybridization oven, only if
connected.

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 Chapter 2 | System Overview 18

Alert and Alert Details Panes

The Alert pane (Figure 2.10) provides alerts if a component or process is not operating as expected.

Figure 2.10 Alerts panes

When you click on an alert in this pane, information about the alert is shown in the Alert Details pane
(Figure 2.11).

Figure 2.11 Alerts Details panes

Alert information may contain:

 Specimen ID

 Assay Name

 Workflow Step

 Date/Time

 Alert Details

 Recommended resolution

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Chapter 3
System Operation Basics

Before you Begin

Read this entire manual and familiarize yourself with the software and procedures.

In this chapter:
 Start and Shut Down the System

 Change Password

 Use of the Barcode Reader

 Edit Multiple Fields in AMDS

 How to Hold Array Cartridges

 E-Signatures

Start and Shut Down the System

Start the Workstation

Turn on the computer workstation to launch the Affymetrix® Molecular Diagnostic Software (AMDS).
AMDS performs:
 A system self-test to confirm the operational status of the system and ensure that all components are
connected and operating correctly
 Housekeeping tasks to ensure that all test requests are in known states and can be processed

When AMDS completes the self-test, the AMDS User Logon window opens.

Log onto AMDS

1. Obtain your User Name and Password from your Affymetrix service engineer or your system
administrator.
2. Login (Figure 3.1):
A. Enter your User Name.
B. Enter your Password.

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 Chapter 3 | System Operation Basics 20

C. Click Log On.

Figure 3.1 AMDS User Log On

AMDS authenticates your credentials and provides functionality based on your user role.

Start the Fluidics Station and Scanner

When your test requests have reached the associated worklists, turn on the fluidics station and scanner.
Scanner laser takes about 10 minutes to warm up.

WARNING: Laser in use during scanning.

IMPORTANT: To preserve the lifetime of the scanner laser, turn off the scanner when it is not
in use for an extended period of time, such as overnight or a weekend.

Log Off
Logging off does not terminate the active workflow processes. If there are test requests in hybridization,
fluidics or scanning, AMDS continues to process them.
1. Go to User Details pane (Figure 3.2)

Figure 3.2 The User Details Pane

2. Click Log Off.

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 Chapter 3 | System Operation Basics 21

Shut Down
1. Go to User Details pane.
2. Click Shut Down.
3. Turn off instrumentation.

IMPORTANT: If there are test requests in progress, a confirmation dialog box opens. Click
Yes to initiate an orderly shutdown of the system. All tests requests that are “In Progress”
go into an error state and must be re-run.

Change Password
1. Go to User Details pane.
2. Click Change Password.
3. In the Change Password dialog box, enter your old password (Figure 3.3).

Figure 3.3 Change Password dialog box

4. Enter and confirm your new password.

5. Click OK.

Use of the Barcode Reader

Use the barcode reader to:
 Enter a Specimen ID for a test request

 Associate a test request with an Array ID

 Associate a test request with reagent lot numbers

 Associate an array with a fluidics station and module

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 Chapter 3 | System Operation Basics 22

Edit Multiple Fields in AMDS

Contiguous Select and Enter

1. Click on first row of your selection.
2. Press and hold Shift key.
3. Click on last row of your selection.
4. Press and hold Ctrl key and:
 Select from drop-down in last row

or
 Click in field in last row and scan barcode

or
 Click in field in the last row, release the Ctrl key, and enter value

5. Click outside field.

Non-Contiguous Select and Enter

1. Click on first row of your selection.
2. Press and hold Ctrl key.
3. Individually select each row.
4. While holding Ctrl key:
 Select from drop-down in last row

or
 Click in field in last row and scan barcode

or
 Click in field in last row, release Ctrl key, and enter value

5. Click outside field.

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 Chapter 3 | System Operation Basics 23

How to Hold Array Cartridges

The array comes mounted in a plastic package to form an array cartridge (Figure 3.4). The array contains
oligonucleotide probes on the inner glass surface. A chamber in the plastic package directly under the
chip acts as a reservoir where hybridization and washing and staining occur.

Figure 3.4 Array Cartridge

Plastic cartridge Notch Septa

Front

Probes on a
glass substrate
Back

Although the inner glass surface is protected, any contamination or scratches on the outer surface of the
glass can compromise the integrity of the scan.

IMPORTANT: Do not touch the surface of the glass with your fingers. Skin oils and other
substances, such as lotions or ink, can fluoresce. If the array surface is dirty, carefully clean it
with a nonabrasive laboratory tissue

E-Signatures
E-signatures help track user activity on the system. At times after completing procedures in AMDS, you
are prompted to confirm a change with your password and the reason for the change (Figure 3.5).

Figure 3.5 E-Signature Confirmation Dialog

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Chapter 4
Running Test Requests

Introduction
A test request is a unique record of an assay performed on a particular specimen. Repeated runs of the
same specimen require multiple test requests. Each test request is associated with a unique array cartridge.

Before you Begin

Read this entire manual and familiarize yourself with the instrument, software, and procedure.

In this chapter:
 Working with Test Requests

 Register a Test Request

 Oven Hybridization

 Wash and Stain Arrays in the Fluidics Station 450Dx v.2

 Scanner 3000Dx v.2

 Data Processing

 Non-Active Worklist

Working with Test Requests

NOTE: Throughout test request processing, you must enter data related to the test request–
use the barcode reader whenever possible.

Active Worklist
The Active Worklist contains all active test requests, regardless of their step in the workflow. After all
steps of the workflow are complete, you can approve or reject test request results from the Active
Worklist. Once approved, rejected, or canceled, test requests are shown in the Non-Active Worklist.

Enter a Test Request

Create Test Request
1. Click Active Worklist (Figure 4.1).

Figure 4.1 Active Worklist Button

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 Chapter 4 | Running Test Requests 25

2. In Active Worklist, click Create (Figure 4.2).

Figure 4.2 The Active Worklist

NOTE: You can create more than one test request at a time.

3. In Enter Test Request window, enter the Specimen ID barcode using the barcode reader (Figure 4.3).

Figure 4.3 The Enter Test Request window–submit

NOTE: If your specimen does not have a barcode, manually enter the name of the
Specimen ID in the Specimen ID field. Specimen IDs need not be unique and can have up
to 40 characters.

4. Under Assay Name, click a down-arrow and select an Assay Name from the drop-down list.
5. Click Submit.
Note that:
 You can submit one or more test requests at the same time after all Specimen IDs and Assay Names
are entered.
 When you click Submit your test request is created and becomes active.

 The Enter Test Request window always closes after you click either Submit or Delete.

 You can find your newly created test request in the Active Worklist based on the Specimen ID, Assay
Name, and current status.

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Delete a Test Request

1. Select test request rows to delete.
2. Click Delete (Figure 4.4).

Figure 4.4 The Enter Test Request window–delete

NOTE: If you delete your test request before you click Submit, the test request is not
created.

Edit a Test Request

You can edit the Specimen ID for a test request only before registration.

Edit Test Request

1. In Active Worklist, select a test request.
2. Click Edit (Figure 4.5).

Figure 4.5 Active Worklist–edit

3. Edit the Specimen ID–this is the only field you can edit.
4. Click anywhere on the tool bar or Specimen ID row.
5. Click Save Changes.
6. In the Confirm Step dialog box (Figure 4.6), enter:
 Your password

 Reason for change

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 Chapter 4 | Running Test Requests 27

Figure 4.6 Confirm Step Dialog Box

7. Click OK.
The edited Specimen ID is now shown on the Active Worklist.

Undo Changes
1. To undo your changes, click Discard Changes (Figure 4.7).

Figure 4.7 Discard Changes on toolbar

2. In the Edit Test Request Confirmation dialog box, click Yes.

After you click Yes, you remain on the Edit Test Request Screen and can continue editing the
Specimen ID.

Cancel All Edits

To cancel edits and close the Edit Test Request window, click Cancel Edit.

Batch Edit a Test Request

IMPORTANT: Batch editing is possible only with test requests that use the same Assay
Software Module (ASM). Batch Edit works only when no arrays associated with the selected
test requests have started scanning.

You can use Batch Edit to associate information with multiple test request records.

Batch Edit
1. In any worklist, select one or more test requests associated with the same ASM.
2. Click Batch Edit.
3. In the Assay Batch Information dialog box, proceed according to your ASM user manual.

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Add Information to a Test Request

You can add data to a test request at any time before its associated array begins scanning. Note that the
dialog box for adding information varies depending on the ASM. You cannot add new fields.

Add Information
1. In any worklist, click on a Specimen ID hyperlink.
2. In the Additional Information dialog box, proceed according to your ASM user manual.

View Assay Information

You can retrieve the information for an assay by going to the Assay Home window. From any worklist,
click on the assay name. For detailed information, refer to your ASM user manual.

Cancel a Test Request

Once you submit a test request you cannot delete it; however, you can cancel it and send it to the Non-
Active Worklist. You can cancel only one test request at a time and only before you generate results.

Cancel Submitted Test Request

1. In Active Worklist, select a test request.
2. Click Cancel Test Request (Figure 4.8).

Figure 4.8 Active Worklist–Cancel Test Request

3. Enter required information in Confirm Step dialog box and click OK.
Affymetrix® Molecular Diagnostic Software (AMDS) moves the test request to the Non-Active
Worklist.

Cancel In Progress Test Request

NOTE: A test request “In Progress” on either the Fluidics or Scanner Worklist cannot be
canceled by the Cancel Test Request button.

1. Click Shut Down to restart your workstation. This action forces all In Progress test requests into an
error state, and stops all processing.
2. In Active Worklist, select a test request.
3. Click Cancel Test Request.
4. Enter required information in Confirm Step dialog box and click OK.
AMDS moves the test request to the Non-Active Worklist.

Register a Test Request

For certain assays, as determined by the assay manufacturer, the system may require additional
information for each test request in order for that test request to run successfully. You must enter this
required additional information before the test request is removed from the Registration Worklist. Refer
to your ASM user manual for details.

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 Chapter 4 | Running Test Requests 29

Associate Test Requests, Arrays, and Reagent Kit IDs

Registration is the association of a test request with the array to be used for that test request. Depending
on the assay, the target preparation reagent kit information may also be collected during this step.

NOTE: Not all assays require a Target Preparation Reagent Lot ID. For some assays, you enter
reagent data using the Reagent Information tab of the Assay Home window. Refer to your
ASM user manual for details.

Register Test Request

1. Click Registration (Figure 4.9).

Figure 4.9 Workflow Panel–Registration

2. In the Registration Worklist, scan the Specimen ID barcode (Figure 4.10). AMDS selects the test
request associated with the Specimen ID.
You can also manually select the Specimen ID from the worklist.

Figure 4.10 The Registration Worklist

3. Scan the array barcode from the array cartridge. AMDS populates the Array ID field.
You can also enter this information manually.

NOTE: An AMDS alert opens if this Array ID is already in use, if the array is expired, or if
the array type is not compatible with the assay type.

4. Optional–Enter the Target Preparation Reagent Kit ID.

See your ASM user manual for information about entering reagent information for your assay.
5. Click Save.
6. Click Complete Step.

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 Chapter 4 | Running Test Requests 30

This step completes the registration and moves the test requests to the next step in the workflow,
which depends on the type of assay you are using. Refer to your ASM user manual for details.

NOTE: Some assays require additional information for test requests. The required
information must be entered before the test request moves off the Registration Worklist.
Refer to your ASM user manual for details.

Troubleshooting Registration
You must correct the data entry if you get a message that:
 The Array ID already exists

 You have entered an invalid Array ID

 The array is expired

 The Reagent Kit ID entry is disabled for this assay

 The Reagent Kit ID entered is invalid for this assay

You cannot complete registration until you correct the error.

Oven Hybridization

Set Up Oven Hybridization

Enter Oven Information

IMPORTANT: Make sure you understand how to operate your hybridization oven.

NOTE: You cannot change any parameter in the Time/Rotation/Duration field in the
Hybridization Oven Worklist. These are the optimal hybridization parameters for the assay.

1. Click Hybridization Oven (Figure 4.11).

Figure 4.11 Workflow–Hybridization Oven

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 Chapter 4 | Running Test Requests 31

IMPORTANT: Follow the Step 2 only if you are using an oven tray.

2. In Hybridization Oven Worklist (Figure 4.12), associate test requests with an oven tray.

Figure 4.12 The Hybridization Oven Worklist

A. Scan the array barcodes.

B. Scan barcode for associated tray.

NOTE: To enter the tray number by hand:

1. Select the test requests.
2. Enter a tray ID.

3. Select all test requests for the arrays you place into the oven.
 Select one test request for a tray and click Select Tray

or
 Manually select test requests

4. Enter the oven number.

 For a connected oven, enter 1 or 2, depending on your oven setup

or
 For an unconnected oven, enter E

5. Click outside field to populate oven number for all selected Specimen IDs.

Start and Monitor Hybridization

You can place your arrays into an oven that is hybridizing other sets of arrays only if the oven temperature
and rotation speed are correct for your arrays.
1. Turn oven on.
2. Wait until it reaches hybridization temperature.
3. Place array cartridges into trays.
4. Place trays into hybridization oven.
5. Select test request(s) in Hybridization Oven Worklist.
6. Click Start.

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 Chapter 4 | Running Test Requests 32

7. Monitor hybridization process using Hybridization Oven Worklist.

NOTE: The background color of the Reported Elapsed Hybridization Time cell turns yellow
when the time is less than the minimum time required by the assay parameters, green
when it falls within the acceptable range, and red when it exceeds the maximum
allowable time.

End Hybridization
1. Upon completion, remove arrays from oven.
2. Select test requests associated with the arrays.
3. Click End.
4. Click Complete Step.
The test requests move to the Fluidics Worklist.

Hybridization Errors
AMDS checks your data as you enter the tray and oven information.
You must correct the issue if you get an error message that arrays are not compatible for:
 Inclusion on same tray

 Current temperature and rotation speed of oven

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 Chapter 4 | Running Test Requests 33

Wash and Stain Arrays in the Fluidics Station 450Dx v.2

IMPORTANT: Ensure correct operation of your fluidics station. Refer to the GeneChip® System
3000Dx v.2 User Guide.

Preparation
Set Up Fluidics Station
1. Click Fluidics (Figure 4.13).

Figure 4.13 The Fluidics Button

2. In Fluidics Worklist, click Station Setup (Figure 4.14).

Figure 4.14 The Fluidics Worklist

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 Chapter 4 | Running Test Requests 34

Fluidics Station Setup window opens (Figure 4.15).3

Figure 4.15 The Fluidics Station Setup screen

3. Under Assay Name, select an assay for each fluidics stations you will use.
4. Enter Wash Buffer A and Wash buffer B lot numbers (optional).
5. Under Station #, select fluidics station(s).
6. Click Prime Fluidics Station and follow fluidics station LCD instructions.

IMPORTANT: Prime fluidics station when your first start it, change wash buffers, after a
shutdown, or if resolution to an alert requires priming.

7. Click Close Setup Screen.

Associate Test Requests

Associate Test Requests with a Fluidics Station
1. Click Fluidics.
2. Place array in fluidics station module. Do not load cartridge yet.
3. Associate test request with fluidics station module.
A. With barcode reader:
1) Scan array barcode.
AMDS selects correct array and gives a single “ding.”
2) Scan barcode for associated fluidics station module.
AMDS enters information and gives a double “ding.”
B. Manual entry:
1) Select a test request record with correct Array ID.
2) Enter fluidics station number in Station # field.
3) Enter module number in Module # field.

3 All modules are checked by default. Checked modules are used if the station is used; unchecked modules are not used if the
station is used.

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 Chapter 4 | Running Test Requests 35

Start Fluidics Run

1. In Fluidics Worklist, select test requests.
2. Click Start.
3. Follow instructions on fluidics station LCD.
4. When done, remove arrays.
5. Click Complete Step.
The test request(s) move to the Scanner Worklist.

NOTE: If you are done processing arrays for this assay or will not use fluidics station for
several hours, shut down the fluidics station.

Scanner 3000Dx v.2

IMPORTANT: Ensure correct operation of your scanner. Refer to the GeneChip® System
3000Dx v.2 User Guide.

Normal Operational Mode

Scan Arrays
1. Click Scanner (Figure 4.16).

Figure 4.16 Scanner Worklist Button

The Scanner Worklist window opens (Figure 4.17).

Figure 4.17 The Scanner Worklist

2. Load array cartridges into AutoLoaderDx v.2–start with slot 1 and load contiguously.
3. Click Start.
4. When done, click Complete Step.

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 Chapter 4 | Running Test Requests 36

Scanner Status Error

You may see “Socket Error 0” in the Device Status pane if you turn off the scanner while AMDS is still
running (Figure 4.18).

Figure 4.18 Scanner socket error

Perform the following procedure.

1. To reconnect to the scanner, go to the Scanner Worklist and click Disconnect Scanner.

IMPORTANT: Do not click Disconnect Scanner during scanning.

Figure 4.19

Scanner status changes to “Not Connected.”

Figure 4.20

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 Chapter 4 | Running Test Requests 37

2. Click Connect Scanner.

Figure 4.21

Communication is restored.

Figure 4.22

NOTE: If the scanner is powered on when you follow this procedure, the appropriate status
shows in the Device Pane. If the scanner is powered off, status is not updated until the
scanner is powered on.

Manual Mode

NOTE: You can scan one array at a time using the manual scan function. Manually scan arrays
that have illegible or missing barcode labels. AMDS attempts to scan the barcode and validate
that the selected test request is correct.

Scan Arrays
1. Click Scanner.
2. Open AutoLoaderDx v.2 door.
3. Insert array into AutoLoaderDx v.2 carousel at slot 1.
4. Close door.
5. Select correct test request on Scanner Worklist.
6. Click Manual Scan (Figure 4.23).

Figure 4.23 The Scanner Worklist

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 Chapter 4 | Running Test Requests 38

7. When door unlocks, open door and remove array.

8. Click Complete Step.

Stop a Scanner Run

To add arrays to the carousel or if issues occur, you can stop the scanner in the middle of a scanner run.
1. Click Stop Scan.
2. When door unlocks, open door and:
 Add array(s)4

or
 Remove array(s)

3. Click Start to resume scanning with array in slot 1.

NOTE: Scanner does not rescan any previously scanned arrays and always starts the run
with slot 1.

4 To add arrays, remove scanned arrays and consolidate unscanned arrays. Start with slot 1 and load contiguously.

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 Chapter 4 | Running Test Requests 39

Data Processing
AMDS processes the scanned data by:
 Taking resulting DAT file

 Applying a grid

 Generating intensity data

 Generating a CEL file

The CEL file is analyzed according to the ASM in use.

When processing is complete, an “Awaiting Review” hyperlink (Figure 4.24) opens in the Review Results
column of the Active Worklist or the test request moves to the Non-Active Worklist, depending on the
ASM in use.

Figure 4.24 The Review Results Function

Review Test Results

NOTE: The review workflow for test results is assay dependent. Refer to your ASM user
manual for instructions on finalizing your test request(s).

Review Results
1. Click Active Worklist.
2. Click Awaiting Review (Figure 4.24).
A Results window for your particular assay opens.

Non-Active Worklist
View test requests on the Non-Active Worklist:
 When test requests were canceled before processing finished

 After processing finished but before test requests are archived and purged

Once you archive and purge a test request, you can only view it from CD/DVD or the network location
of the archive.To view non-active test requests, click Non-Active Worklist (Figure 4.25).

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 Chapter 4 | Running Test Requests 40

Figure 4.25 Non-Active Worklist Button

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Chapter 5
Troubleshooting

In this chapter:
 Types of Errors

 Resolving Alerts

 Instrument Troubleshooting

Types of Errors
There are three general types of errors that may occur:
 Instrument–For example, communication issues with the hybridization oven, problems with a fluidics
station or module, or problems with the scanner (also refer to the GeneChip® System 3000Dx v.2 User
Guide)
 Test Request–For example, the barcode of the array associated with a test request cannot be read, or a
test request gridding failure
 Operational–These include data input errors

Affymetrix® Molecular Diagnostic Software (AMDS) tracks and reports on all three error types.

Instrument Errors
If you suspect an instrument issue, view the Device Status pane (Figure 5.1).

Figure 5.1 Device Status Pane

Check the device status column to see if there are instrument errors.

NOTE:
 Occasionally an instrument issue occurs and no alert is evident in AMDS. One example is a
leaking fluidics module. If you are not sure how to handle an issue and there is no alert with
a recommended resolution, turn off the instrument and contact Affymetrix support.
 In some cases you may not be able to resolve an instrument problem. You are directed to
contact Affymetrix support to resolve the problem. Do not attempt to correct this kind of
problem yourself.

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 Chapter 5 | Troubleshooting 42

Device Status Icons

 Green Check Mark—Device is ready

 White Circle with Green Arrow—Device is running correctly

 Yellow Triangle—Check the Alert and Alert Details panes

 Red Circle with Slash—Device is not connected

 Red Circle with White x—Device is turned off or attempting to connect

View Alerts and Alert Details

The Alerts pane (Figure 5.2) gives short descriptions of errors. Hover your mouse cursor over the
description to view a ToolTip with the full error description.

Figure 5.2 Alerts Pane

Click on the alert in the Alerts Pane to view the corresponding alert details on the Alert Details pane.
The Alerts Details pane (Figure 5.3) gives a full description and suggestion for corrective action.

Figure 5.3 Alert Details

Test Request Errors

Issues with a test request generate an alert with an associated Specimen ID and module.These include:
 Scanner error reading barcode

 Autofocus error

 Gridding error

 Analysis algorithm error due to missing information

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 Chapter 5 | Troubleshooting 43

Operational Errors
Operational are relatively easy to detect and correct because AMDS gives immediate feedback in order
to prevent incorrect operation and/or data input. Some examples are:
 Invalid array barcode entry

 Array loaded onto unprimed fluidics station

 Array loaded onto fluidics station configured for a different assay type

 Array scanned while its test request is in the Fluidics Worklist

Resolving Alerts
IMPORTANT: Resolve alerts as soon as they occur. This practice makes it easier to decipher
new alerts as they appear.

1. In the Alerts pane, click on the alert.

2. Follow the suggested resolution procedure given in the alert details.

NOTE: If the alert concerns a Specimen ID, click Go to test request to select the row in the
worklist that contains the related test request.

3. Click Resolve.
4. At the prompt, enter your password and additional information.
5. Click OK to remove the alert from the list.

NOTE: If after completing the recommended resolution procedure you are unable to
resolve the error, call Affymetrix support.

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 Chapter 5 | Troubleshooting 44

Instrument Troubleshooting
Table 5.1
Problem/Error Resolution

Fluidics Station 450Dx v.2

Not primed Go to the fluidics setup pane

Prime the fluidics station for the selected assay class

Configured for a different assay Go to the fluidics setup pane

Prime the fluidics station for the selected assay class
or
Determine which fluidics station is configured for the assay type

Missing fluid Possible cause: Insufficient quantities of fluids or the wrong fluids are provided.
Determine the source of the problems on the fluidics station LCD
Follow the resolution procedure in the alert details
Clear the alert, and continue the fluidics run
If you continue to see this error, it may indicate a system failure. Call Affymetrix technical support.

Scanner 3000Dx v.2

Autofocus Possible cause: Array cartridge glass substrate is smudged or dirty, usually from a thumb print.
Clean the array
Clear the alert
Retry

Barcode could not be read Retrieve the array

Process using the manual scan procedure

Monitor/User Interface

Entire AMDS screen not visible; Set back screen resolution to the default using the correct key combination for your style monitor:
cannot interact with complete User  Wide-screen Monitor–Ctrl+Alt+W

Interface  4:3 Monitor–Ctrl+Alt+R

NOTE: These two keystroke combinations have no effect if used on the wrong monitor (e.g., if
Ctrl+Alt+W is used on the 4:3 monitor).

Scanner Status Error

You may see “Socket Error 0” in the Device Status pane if you turn off the scanner while AMDS is still
running (Figure 5.4).

Figure 5.4 Scanner socket error

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 Chapter 5 | Troubleshooting 45

Perform the following procedure.

1. To reconnect to the scanner, go to the Scanner Worklist and click Disconnect Scanner.

Figure 5.5

Scanner status changes to “Not Connected.”

Figure 5.6

2. Click Connect Scanner.

Figure 5.7

Communication is restored.

Figure 5.8

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 Chapter 5 | Troubleshooting 46

NOTE: If the scanner is powered on when you follow this procedure, the appropriate status
shows in the Device Pane. If the scanner is powered off, status is not updated until the
scanner is powered on.

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Appendix A
AMDS Administrative Features

This Appendix gives the Administrative features in Affymetrix® Molecular Diagnostic Software
(AMDS).

In this appendix:
 View Logs

 Manage Assays

 Manage Users

 Manage the System

Access administrative features in the Administrator pane (Figure A.1). User privileges are defined by user
role–if a button is disabled, you do not have access to that feature.

Figure A.1 Administrator Pane

View Logs

System Logs
System logs contain system-level algorithm and computer messages, as well as recorded parameters of
completed assays, such as date and time, component, type, user, etc. To view the current system log, click
View Logs in the Administrator pane (Figure A.1). The system log is shown in the top position.
To view a system log other than the current one, select one from the System Log list.

Filter System Log Entries

1. Select a system log.
In subhead row, enter filter criteria (Figure A.2). Filter by:
 Date/Time

 Component

 Type

 User

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 Appendix A | AMDS Administrative Features 48

Figure A.2 View Logs window

To show all log entries, click Remove Filter.

Audit Logs
Audit logs contain information, messages, and parameters for a test request for each step of the workflow.
The Audit Log is found below the System Log in the View Logs window (Figure A.3).

Figure A.3 Audit Log

View Audit Log

2. Click Browse for Audit Logs (Figure A.3) to find a log for a test request.

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 Appendix A | AMDS Administrative Features 49

3. In the dialog box (Figure A.4), select the test request.

Figure A.4 Audit Log List

4. Click Display.

Filter Audit Logs

1. Select an audit log.
2. In subhead row, enter filter criteria (Figure A.3). Filter by:
 Date/Time

 Workflow step

 Log message type

 User

Print Audit Logs

1. Select audit log.
2. Click Print (Figure A.3).

Export and Burn Log Files to CD or DVD

NOTE: You can burn log files only to the workstation internal CD/DVD drive.

While viewing either a system or audit log, click Export to send the entire log file to the export queue.
The View Logs toolbar shows the total size and number of logs in the queue.

Export Log Files

For each system and audit file you want to export:
1. Select the file.
2. Click Export.
The View Logs tool bar increases the number of exported files by 1. The entire unfiltered log file is
exported.

Burn Log File to CD or DVD

To export the current list to the CD/DVD drive, click Burn (Figure A.5). All queued log files burn to
the disc drive.

Figure A.5 Burn button

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 Appendix A | AMDS Administrative Features 50

Manage Assays
Assay Management enables you to install, repair, or deactivate assays or install SSL certificates.

NOTE: You must be logged in as a Laboratory Supervisor or System Maintainer to install an

assay or certificate.

Install an Assay
Typically, an Affymetrix field service engineer installs assays and certificates. If an assay communicates
with a remote server and the certificate for that server has not been installed in AMDS, you must install
the server certificate first (refer to your ASM user manual to determine if you need to install the
certificate). To install an assay, you must have the assay installation bundle, which is typically provided
on a CD.

Install Assay
1. Click Assay Management (Figure A.6).

Figure A.6 Administrator Pane

The Assay Management window opens (Figure A.5).

Figure A.7 The Assay Management screen

2. Place CD with ASM installation bundle into the workstation CD/DVD drive.
3. Click Install Assay.

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 Appendix A | AMDS Administrative Features 51

4. In the Assay Installation dialog box (Figure A.8), go to Select the Manifest file and enter or browse
to the manifest file (part of the assay installation bundle).

Figure A.8 The Assay Installation dialog box

5. Select users permitted to run this assay.

6. Click Install.

Deactivate an Assay
You can deactivate an assay if you no longer use this assay and do not want it to appear as a selection in
the AMDS application. There is no uninstall mechanism for an assay.
1. In the Assay Management window, select an assay.
2. Click Deactivate (Figure A.5).
Once you deactivate an assay, you can still complete the workflow for any active test requests for this
assay. However, the assay is no longer available for entering new test requests.

Repair or Reactivate an Assay

To repair or reactivate an assay, reinstall the assay as for a new install.

Install a Server Certificate

Some assays require data transfer to a remote system during analysis. As a security measure, AMDS may
require that you or your Affymetrix field service engineer install an SSL server certificate on your local
workstation, depending on the transfer protocol used.
If a correct certificate is not installed you can still install the assay and process test requests; however,
because you do not have permission to access the remote server, you cannot transfer test request data to
the remote server.
If you have installed a certificate but cannot access the remote server, contact Affymetrix technical
support.

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 Appendix A | AMDS Administrative Features 52

Install a Certificate
1. In the Administrator pane, click Assay Management (Figure A.9).

Figure A.9 Administrator Pane

2. In the Assay Management window, click Install Certificate (Figure A.10).

Figure A.10 The Assay Management screen

3. In the Server Certificate dialog box (Figure A.11), select:

 Install from CD

or
 Install from local disk drive

Figure A.11 Server Certificate Dialog

4. Navigate to and select a .cer file (the certificate has a .cer extension).
5. Click OK1.
If it is a:
 Successful installation–The message “You have successfully added the server certificate ‘x.cer’ to the
AMDS trusted certificate store” opens

1 Or click Cancel to end the installation.

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 Appendix A | AMDS Administrative Features 53

or


 Failed installation–AMDS notifies you with an algorithm message. You are not permitted to access
the server and transfer data.
6. Click OK.

Manage Users

AMDS User Roles

Each user has a defined role that specifies the actions the user is allowed to perform on the system.
 Guest–Allowed to view non-patient information. Not allowed to perform any processing steps for a
test request. A Guest should not be given access to any ASMs.
 Technician–Can create test requests and process them through the workflow. Cannot approve or reject
test request results.
 Technologist–Can create and process test requests through the workflow, and can approve or reject
results.
 System Maintainer–Can access all System Management windows and perform tasks like archiving test
requests, maintaining instruments, and general system configuration. Cannot perform any test request
processing steps and cannot view patient data. A System Maintainer should not be given access to any
ASMs.
 Laboratory Supervisor–Can perform all tasks of a Technologist and all tasks of a System Maintainer.

Add a User
Before you add a user, review the AMDS user roles.
If there are no assays installed on the system, you do not have the option of granting assay access to a user.

Add User
1. In the Administrator pane click User Management (Figure A.12).

Figure A.12 Administrator Pane

2. In the User Management window, click Add User (Figure A.13).

Figure A.13 User Management window

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 Appendix A | AMDS Administrative Features 54

3. In the Add User window, establish new user characteristics (Figure A.14).
 Active–Indicates whether or not the user account being created at this time is active

 Enter a User ID

 Enter First Name

 Create a Password

 Confirm Password

IMPORTANT: Password must comply with the local security policy on the AMDS
workstation. This policy is determined by your IT department.

Under Select Role, select user role



Under Select Assay Group(s), select assay groups for the user.


4. Click Save Changes (Figure A.14).

Figure A.14 Add User window

Edit a User
You can change any user attribute except User ID.
1. In the User Management window, select a user.
2. Click Edit User.

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 Appendix A | AMDS Administrative Features 55

3. In the Edit User window, make edits (Figure A.15).

Figure A.15 Edit User Window

4. Click Save Changes.

Deactivate a User
To deactivate a user, got to the Edit User window and deselect Active. The account can be reactivated.

Manage the System

Change System Management Windows

Use the System Management menu to move among system management windows.

Change Windows
1. In Administrator pane, click System Management (Figure A.16).

Figure A.16 Administrator Pane

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 Appendix A | AMDS Administrative Features 56

2. Click In-House Service and select a function (Figure A.17).

Figure A.17 System Management menu

 User Performed Service–View system configuration (i.e., device and instrument settings) and manage
Fluidics Station 450Dx v.2, workstation, Scanner 3000Dx v.2, printer, and firewall
 Service Logs–View logs of user-performed services
 Archive Test Request–Archive and purge test request data.
 General Configuration–Change time and time zone settings for your location and configuration flags
for your instruments, and set up network archive location

Manage Instrument Settings

User Performed Service functions are:
 Remote troubleshooting session

 Export of troubleshooting data

 Manage Fluidics Station(s) 450Dx v.2

 Manage system hard drive

 Manage printer

 Manage firewall

Remote Troubleshooting Session

Enables troubleshooting and resolution by an Affymetrix service technician.
1. Contact your Affymetrix service technician.
2. Log in as User with System Maintainer or Laboratory Supervisor privileges.
3. In Administrator pane, click System Management.
4. In User Performed Service window, click Start Remote Session.

Figure A.18 User Performed Service window

5. In Confirm Step dialog box, enter your password, then click OK.

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 Appendix A | AMDS Administrative Features 57

The Allow Remote Control window opens (Figure A.19).

Figure A.19 Allow Remote Control window

6. Give Your ID and Password from this window to the service technician. This enables the Service
Technician to remotely connect to your system to diagnose or resolve your issue.
The service technician connects remotely. The Session list window (Figure A.20) remains on your
computer window while the remote session is in progress.

Figure A.20 Session list

Export Troubleshooting Logs

Your Affymetrix service technician may need troubleshooting logs to aid in the diagnosis and resolution
of your issues.
1. Click Export Troubleshooting Logs (Figure A.21)

Figure A.21 User Performed Service window

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 Appendix A | AMDS Administrative Features 58

2. In the Stating Support Log Files dialog box (Figure A.22), enter a brief message and/or a text string
to append to the file name.

Figure A.22 Staging Support Log Files

3. Insert a CD or DVD into the system drive.

4. Click Yes.
A zip file containing all the logs is created and saved to the CD/DVD.
5. When done, eject the CD/DVD.
6. Insert the CD/DVD into a non-AMDS computer
7. Provide the zip file to your Affymetrix service technician.

Manage Fluidics Station 450Dx v.2s

Perform the following functions under Fluidics Station in the User Performed Service window
(Figure A.23).

Figure A.23 Fluidics Station region of User Performed Services window

NOTE: Before(s) proceeding, go to Station and select a fluidics station from the drop-down
list.

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 Appendix A | AMDS Administrative Features 59

 Check elapsed time–Under Time Elapsed Since, view days elapsed since last bleach or tube change
 Bleach protocol–under Procedure, select Bleach, click Perform, then follow bleach procedure.
 Change tubing–Under Procedure, select Change Tubing and follow change tubing procedure (refer to
the GeneChip® System 3000Dx v.2 User Guide), then click Perform.
 Troubleshoot or test communication–Under Procedure, select Home, then click Perform.
 View or change Bleach Interval Warning Limit and Bleach Interval Alert Limit–Go to Configuration to
set limits, then click Save. Note:
 Beach reminder schedule is preconfigured by Affymetrix

 Warning times must be less than alert times

 Change alert first, then warning

 View or change Change Tubing Warning Limit and Change Tubing Interval Alert Limit–Go to
Configuration to set limits, then click Save. Note:
 The change tubing reminder schedule is preconfigured by Affymetrix

 Warning times must be less than alert times

 Change alert first, then warning

Manage Workstation Hard Drive

Perform the following functions under System in the User Performed Services window (Figure A.24).

Figure A.24 The System Region of the User Performed Services Screen

 HDD Space Available–View available space on workstation hard disk

 Export File Size–View size of current export files; to clear list without burning to disc, click Clear.
 Configuration–View or change HDD Space Warning Limit or HDD Space Alert Limit
 Space alert limit must be less than warning alert limit

 Change alert first then the warning

 Cannot set alert below system-determined percentage

IMPORTANT: Alerts warn when workstation hard drive nears capacity. Archive and purge
data before system reaches limit. At alert limit, AMDS does not scan arrays and you must
archive and/or purge data to stay below limit.

 Restart Scanner–Click if you are experiencing problems connecting to the Scanner 3000Dx v.2
 Check Network Archive Storage Free Space–Click to view available space on Network Archive location
(if applicable)

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 Appendix A | AMDS Administrative Features 60

Manage Printer
Perform the following functions under Printer in the User Performed Services window (Figure A.25)

Figure A.25 The Printer region of the User Performed Services screen

 Printer Name–Gives printer name

 Online/Offline–Select to change status
 Offline disables print button

 Online enables print button

 Number of Jobs in Queue–Gives number of jobs

 Purge All–Click to remove all print jobs from queue
Click Purge All to remove all the jobs from the print queue.
 Resume All–Click to resume jobs in queue

NOTE: You cannot change the printer. An Affymetrix field service engineer sets up the printer
as part of the AMDS installation process.

Firewall Settings
The AMDS firewall monitors incoming and outgoing messages from the workstation and protects the
workstation from malicious intrusion.
Perform the following functions under Firewall in the User Performed Services window (Figure A.26).

Figure A.26 Firewall region of the User Performed Services window

 Last Backup–Shows date and time of last firewall backup

 Backup–Click to back up current firewall settings
 Restore–Click to restore firewall settings from last backup

NOTE: Some assays access servers on an intranet or on the internet. When these assay
software modules are installed, a rule is written to the firewall that permits communication
between the AMDS workstation and the remote server. Restoring firewall settings may
overwrite these rules and prevent AMDS from communicating with the server. In this case,
reinstall any ASMs that communicate with remote servers in order to restore communication
between the workstation and server.

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 Appendix A | AMDS Administrative Features 61

View User Performed Service Logs

NOTE: Do not confuse the View Service Log function with the View System and Audit logs
that are described in the section View Logs on page 47.

A User Performed Service Log entry is created for most of the actions you perform on the User Performed
Services window. You can open and view these service logs.
8. In System Management menu, select User Performed Service Logs (Figure A.27).

Figure A.27 System Management menu

9. In User Performed Service Log (Figure A.28), filter by:

Figure A.28 View User Performed Service Log

Date/Time
 Procedure

 User

 Device

 Description

10. Click Remove Filter to view all log entries.

Archive and Purge Test Requests

IMPORTANT: Once test requests are purged they cannot be restored to AMDS. They are
available only on the CD/DVD containing the archive, any print outs, or similar material.

Perform the following functions in the Archive Test Requests window.

 View test requests

 In AMDS, ready to be archived

 On a CD/DVD containing an archive

 Filter the archive

 Archive test requests to CD/DVD or network location

 Purge selected test requests

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 Appendix A | AMDS Administrative Features 62

View and Filter Test Request Archives

You can view test requests that have been archived to
 CD/DVD by clicking DVD Index (Figure A.30)

 Either CD/DVD or a network location from a non-AMDS workstation

1. In the System Management menu, select Archive Test Requests (Figure A.29).

Figure A.29 System Management menu

The Archive Test Request window opens (Figure A.30).

Figure A.30 Archive Test Requests window

Note that:
 If a test request has a green checkmark in the Archived DVD or Network column, it has been
successfully archived
 The System Management tool bar gives the total number of tests that are ready to be archived

2. Click:
 AMDS Index to view test requests in AMDS that are ready to be archived

or
 DVD Index to view test requests from an archive CD/DVD

The disc must be in the workstation disc drive.

3. Filter the index by:
 Date completed

 Assay name

 Array ID

Archive Test Requests

Archiving logs is different than exporting logs. When you archive to a network drive or CD/DVD, you
archive only selected test requests. Exported logs are not burned to a disc when archiving test requests.
To archive, select test requests. The number of test requests you select are shown on the toolbar. Click:
 DVD Archive to burn the selected test requests to CD or DVD

or
 Network Archive to archive to a remote drive

NOTE: The network drive must be configured for this feature to be available.

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 Appendix A | AMDS Administrative Features 63

Purge Test Requests

To purge, select the test request(s) and click Purge (Figure A.31).

Figure A.31 Archive Test Requests window

You can purge a test request record only after it has been archived. Once test requests have been purged,
they are no longer available on the AMDS system.

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 Appendix A | AMDS Administrative Features 64

Set General Configurations

Perform the following functions in the General Configuration window (Figure A.32).

Figure A.32 General Configuration screen

 View System Configuration Summary report

 View and configure time and time zone settings
 Configure Scanner 3000Dx v.2 settings
 Require users to approve or reject analysis results before proceeding
 Configure network archive location settings

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 Appendix A | AMDS Administrative Features 65

View System Configuration Summary Report

The System Configuration Summary report provides a snapshot of the current hardware and software
configuration of your system.

Generate Report
1. In the Administrator pane, click System Management.
2. Under In-House, select General Configuration (Figure A.33).

Figure A.33 System Management menu

3. Click System Summary (Figure A.34).

Figure A.34 General Configuration toolbar

The System Configuration Summary Report opens (Figure A.35).

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 Appendix A | AMDS Administrative Features 66

Figure A.35 System Configuration Summary Report - Example

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 Appendix A | AMDS Administrative Features 67

The System Configuration Summary report includes:

 Current date and time

 AMDS Version

 Operating System

 Workstation name

 Scanner 3000Dx v.2 Serial number

 Hybridization Oven Serial Number (if present)

 Fluidics Station 450Dx v.2 and Module Serial Numbers (if present)

 Installed ASM information (if present)

The printed version of this report also contains an Affymetrix Technician Service history log.
To print the report, click Print. If the Print button is not enabled (grayed out), contact your Affymetrix
Service Technician to connect a printer to your system.
To export the report, click Export. If the Export button is not enabled (grayed out), see Configure Network
Archive Storage on page 69. Note that the Export button is enabled only after an archive storage location
is established.

Time Zone Settings

IMPORTANT: Do not change the local time or time zone while test requests are in progress
(on any worklist).

1. View in the Administrator pane, click System Management.

2. Under In-House, select General Configuration.
3. In the General Configuration window, goto the Time Zone Current Settings section.

Configure
1. In the Time Zone Editable Settings change settings.
A. In Editable Local time, set local time.
B. In Time Zone, set local time zone.
2. Click Save Changes.

Configure Scanner 3000Dx v.2 Settings

1. In the Administrator pane, click System Management.
2. Under In-House, select General Configuration (Figure A.36).

Figure A.36 System Management menu

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 Appendix A | AMDS Administrative Features 68

3. In the General Configuration window, go to the System Configuration Flags section (Figure A.37).

Figure A.37 System Configuration Flags section

4. Select Turn on Laser to turn on the Scanner 3000Dx v.2 laser automatically when you launch the
AMDS application.
5. Select Disable AutoLoader to disable the Scanner 3000Dx v.2 and manually load/unload arrays from
the Scanner 3000Dx v.2 (refer to Chapter 5 of the GeneChip® System 3000Dx v.2 User Guide).

IMPORTANT: This should be used only if the AutoLoaderDx v.2 has failed and there are
arrays that must be scanned immediately.

6. In the toolbar, click Save Changes.

User Approval for Analysis Results

NOTE: This section is applicable only to ASMs that require report approval. This section is not
applicable to users of Affymetrix ASMs because they do not require report approvals.

Goto the System Configuration Flags window and select Require User Approval to require the technician
to approve or reject the analysis results as they become available after an assay run (Figure A.37). This
flag is meaningful only if you do not want to approve or reject the results on the AMDS system.
Deselecting this option causes the test requests to immediately move to the Non-Active Worklist upon
completion of the analysis algorithm. You cannot view the results through the Active Worklist.

NOTE: This option is intended for use with a Laboratory Information System (LIS). If you select
this option, you must review the results for each test request. If the box is not selected, the
test requests disappear from the Active Worklist upon completion of the workflow and
reappear on the Non-Active Worklist without user intervention.

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Configure Network Archive Storage

1. In the General Configuration window, goto the Network Archive Storage Configuration section
(Figure A.38).

Figure A.38 Network Archive Storage Configuration section

2. Enter a valid information for:

 UNC Share

 User Name

 Password

3. Click Test Connection to configure the firewall and write a temporary file to share.
4. Check Enable archiving to network.

NOTE: If the test fails, an error message provides assistance troubleshooting the problem.

5. Check Use MD5 checksums to verify transfers to get read-feedback verification of archived files.
6. In the toolbar, lick Save Changes.

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Index

A L
Administrative features 47 Logging off 20
Alerts Logs
resolving 43 viewing 47
AMDS
quick reference guide 19 M
Array Molecular Diagnostic System
cartridge 23 administrative features 47
handling 23
scanning 35
N
Assay
deactivating 51 Normal operational scanning mode 35
installation 50
Assay management panel O
selecting assays 51 Operational and data input errors
resolving 43
B
Barcode reader 21 P
Bleach interval alert limit 59 Peristaltic tubing change 59
Bleach interval warning 59 Printer management 60
Probe array handling 23
C Processing test requests 30
Cancelling
test requests 28 R
Configuration panel 59 Resolving
Creating alerts 43
test request 24
S
D Scanner Status Error 36, 44
Deactivate assay 51 Scanning
normal operational mode 35
E Shutting down 21
Edit user 55 Specimen ID
Error, adding additional information 28
operational and data input 43 Stopping a scan 38
resolving device related 41 System
Scanner Status 36, 44 logoff 20
test requests 42 shutting down 21

F T
Fluidics station Technical support 8
using 34
Test requests
additional information 28
H cancelling 27
Hybridizing 30 creating 24
deleting 27
editing 26
I processing 24, 30
In 51 registration 28
Indications for Use 6 resolving errors 42
washing and staining 33
Install assay 50
Troubleshooting 41
Instrument related errors
instruments 44
resolving 41
Instrument troubleshooting 44

IVD
 Index 71

U
User management
add user 53
edit user 55

W
Washing and staining 33

IVD