Thermo Fisher Scientific HT Scanner User guide

P/N 701978 Rev. 2

September 2005

Affymetrix GeneChip® HT Scanner User’s

Guide

For Research Use Only. Not for Use in Diagnostic Procedures.

Trademarks

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

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

Vision®, and The Way Ahead™ are trademarks owned or used by Affymetrix, Inc.

All other trademarks are the property of their respective owners.

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

Scanners

Products may be covered by one or more of the following patents: U.S. Patent Nos.

5,578,832; 5,631,734; 5,834,758; 5,936,324; 5,981,956; 6,025,601; 6,141,096; 6,171,793;

6,185,030; 6,201,639; 6,207,960; 6,218,803; 6,225,625; 6,252,236; 6,335,824; 6,403,320;

6,407,858; 6,472,671; 6,490,533; 6,650,411; 6,643,015; 6,813,567; and other U.S. or foreign

patents.

Copyright

Compliant with directive 2002/96/EC (WEEE)

I

Contents

CHAPTER 1 The HT Scanner 7

INTRODUCTION 9

Intended Use 11

CONVENTIONS USED IN THIS GUIDE 12

ONLINE DOCUMENTATION 13

SAFETY 14

Power Supply 14

Shock and Other Warnings 15

REGULATORY COMPLIANCE 16

Technical Support 18

DESIGN ELEMENTS AND SPECIFICATIONS 18

Illumination System 18

Excitation Filters 19

Imaging 19

Image Digitization 20

Mechanical Design 20

Power 21

Workstation 21

Plate Formats 21

OPERATING THE HT SCANNER 22

Introduction 22

Starting the HT Scanner 23

Checking the Hours of Operation of the Lamp 25

Loading an HT Array Plate into the HT Scanner 25

Unloading an HT Array Plate from the Scanner 26

Shutting the Scanner down 26

Running a Script on the Scanner 27

II GeneChip® HT Scanner User’s Guide

Changing the HT Scanner Configuration 31

Navigating around the HT Array Plate 33

Setting Focus Parameters 33

Laser Focus Setup 38

Setting the Focus Z Offset 42

Purging the Database 45

CHAPTER 2 HT Image Reader 47

INTRODUCTION 49

HT IMAGE READER APPLICATION LAYOUT 49

GETTING STARTED 50

Analysis Options 50

Email Alert Options 50

Publish Database 51

GCOS Mode 51

Invoking An Analysis 51

Rescanning An HT Array Plate 51

ANALYSIS OPTIONS 51

Auto Invocation Parameters 51

Scanner Information 52

Multi-Scan Parameters 52

Analysis Parameters 52

Analysis Results Checks 53

Publish Parameters 53

Results Check Options 55

Email Alerts 57

Invoking an Analysis 58

Menu Commands 60

WORKFLOW STATUS MESSAGES 60

Menu Commands 61

Query Messages 61

Opening an Image File 62

Sub Image Indexing 63

Image Display 64

Contents III

Image Settings 66

Well to Experiment Mapping 67

Creating the Mapping 67

Viewing the Mapping 68

ADVANCED TOOLS 70

Rename Barcode 70

Image Manipulation 71

Deleting Acquisitions 71

MENU COMMANDS 73

Toolbar Buttons 74

CHAPTER 3 HT Image Reader Appendix 77

INTRODUCTION 79

APPENDIX I – GCOS OBJECTS 79

GCOS Experiment 79

GCOS Sample 80

APPENDIX II – DATA ACCESS 80

Files SDK 80

GCOS SDK 80

AADM Schema and SDK 81

Expression Exporter SDK 81

APPENDIX III – FAQ 81

APPENDIX IV – WORKFLOW 88

Workflow 88

CHAPTER 4 Array Reporter 93

INTRODUCTION 95

REPORT OPTIONS 95

IV GeneChip® HT Scanner User’s Guide

GRAPH OPTIONS 96

Colors 96

Graph Type 96

Metrics 96

Reporting On An HT Array Plate 99

Results Visualization 100

Report Display (well graph format) 101

Report Display (bar graph format with properties) 103

Results Display (3D graph format) 103

Application Menu Commands 105

CHAPTER 5 HT Data Transfer Utility 107

INTRODUCTION 109

TASK TRAY MENU 109

Options 110

Directory Monitoring 110

CHAPTER 6 Maintenance and Troubleshooting 113

INTRODUCTION 115

Safety Warnings 115

SCANNING PROBLEMS 116

Failed Scans 116

Focus Problems 116

Centering 116

REPLACING THE LAMP 117

ADJUSTING FOR A CHANGE IN THE NAME OF THE

WORKSTATION 119

REPLACING THE SHUTTER 120

Materials 120

Tools and Equipment 120

Contents V

OPERATION STEPS 121

Remove the Front Panel 121

Remove the Shutter Cover 121

Remove the Shutter Control Cable 122

Displace the Light Shield 123

Remove the Shutter 124

Install New Shutter 124

Replace the Light Shield 125

Re-attach the Shutter Cable 126

Replace the Shutter Cover 126

Replace the Right-hand Front Panel 127

Re-initialize the HT Scanner 127

Index 131

VI GeneChip® HT Scanner User’s Guide

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Chapter 1The HT Scanner

Chapter 1

9

Introduction

The HT Scanner (Figure 1.1) is a high-throughput, high-resolution, automated

epi-fluorescence imaging system that can automatically scan Affymetrix® HT

Array Plates (Figure 1.2). The instrument is packaged in the form of a bench-

top enclosure containing a light source, illumination and imaging optics,

motorized mechanical stages (x, y, and z), a high-resolution CCD detector,

control electronics, and power supplies. The accompanying desktop computer

workstation provides instrument control functions, image data display and

network capability.

Figure 1.1

The GeneChip® HT Scanner

10 GeneChip® HT Scanner User’s Guide

The following chapters (Table 1.1) provide additional utilities for image

analysis.

Figure 1.2

An HT Array Plate.

Table 1.1

Utilities for image analysis

Operating the HT Scanner on page 22 This section describes how to run the HT

Scanner using the HT Scanner Console

application to scan your HT Array Plates.

HT Image Reader on page 47 This section describes using the HT Image

Reader software to analyze the resulting

fluorescence data from the HT Scanner.

HT Image Reader Appendix on page 77 This section provides supplemental

information concerning the HT Image Reader

software.

HT Data Transfer Utility on page 107 This section describes the use of an

application that monitors the directory where

the HT Scanner Console software stores the

image data files generated during acquisition

and transfers the data files to the GCOS

Server for analysis.

chapter 1 | Introduction 11

INTENDED USE

The Affymetrix® GeneChip® HT Scanner is intended to scan HT Array Plates

based on the Affymetrix GeneChip technology to measure fluorescence

intensity levels.

The system is intended to be used only by laboratory professionals trained in

laboratory techniques and on the use of the GeneChip system.

Array Reporter on page 93 The Array Reporter application will display

the expression report statistics for all wells of

a given HT Array Plate. The software will

allow the user to select one of several

statistics for graphing in either the well graph

or bar graph format.

Maintenance and Troubleshooting on page 113 This sections deals with issues that may arise

during the course of operation of the HT

Scanner.

Table 1.1

Utilities for image analysis

12 GeneChip® HT Scanner User’s Guide

Conventions Used in This Guide

This manual provides a detailed outline for all tasks associated with the HT

Scanner. 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 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:

Click Ye s 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 that appears.

Font Styles

Bold fonts indicate names of commands, buttons, options or titles within a

dialog box. When asked to enter specific information, such input appears in

italics within the procedure being outlined.

For example:

1. Click the Find button or select Edit → Find from the menu bar. The Find

dialog box appears.

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.

Screen Captures

The steps outlining procedures are frequently supplemented with screen

captures to further illustrate the instructions given. The screen captures

depicted in this manual may not exactly match the windows displayed on your

screen.

chapter 1 | Online Documentation 13

Additional Comments

Online Documentation

The CD with the HT Scanner includes an electronic version of this user’s guide.

The online documentation 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 online help contains a version of this user’s guide as a Microsoft® HTML

help file.

Information presented in Tips provide helpful advice or

shortcuts for completing a task.

Caution notes advise you that the consequence(s) of an

action may be irreversible and/or result in lost data.

The Note format presents important information pertaining

to the text or procedure being outlined.

Warnings alert you to situations where physical harm to

person or damage to hardware is possible.

14 GeneChip® HT Scanner User’s Guide

Safety

POWER SUPPLY

Figure 0.1

CAUTION

The power supply cord is used as the main disconnect device. Ensure that the

socket outlet is located and installed near the equipment and is easily accessible.

ATTENTION

Le cordon d’alimentation est utilisé comme interrupteur general. La prise de

courant doit être située ou installée a proximité du materiel et être facile

d’accés.

ACHTUNG

Zur sicheren Trennung des Gerätes vom Netz ist der Netzstecker zu ziehen.

Vergewissern Sie sich, daß die Steckdose leicht zugänglich ist.

CAUTION

chapter 1 | Safety 15

Shock and Other Warnings

WARNING: HAZARDOUS VOLTAGE and LASER RADIATION are present within

the scanner.

To prevent electric shock and damage to the instrument, access the optical

compartment only, as described in Maintenace and Troubleshooting.

Remove power from the instrument as instructed prior to any

maintenance or servicing.

Customer servicable components are limited to specified optical

components located in optical compartment only.

Visible laser radiation when top panels are removed. Do not remove the

top panels.

CAUTION: Do not remove lamp immediately after operation.

Allow lamp to cool before replacement. High pressure lamp may explode

if improperly handled. Carefully follow lamp replacement instructions

provided in Maintenance and Troubleshooting.

CAUTION: Lifting hazard. The scanner is a heavy object

If you use the HT Scanner in a manner not specified in this user guide,

you may impair the protection provided by the equipment and possibly

void the warranty.

16 GeneChip® HT Scanner User’s Guide

Regulatory Compliance

The scanner is certified for compliance with the following regulatory standards,

or applicable equivalents, for the United States, Canada, and the European

Union.

Product Safety for “Electrical Equipment for Measurement, Control, and

Laboratory Use”, Pollution Degree 2, Overvoltage Category II:

Low Voltage Directive 73/23/EEC (European Union)

• EN 61010-1:2001

• EN 60825-1:1994+A1:2002+A2:2001 for Class I Laser Devices

The scanner complies with FDA performance standards CFR part 1040.10 for

Class I Laser Devices, per CDRH Laser Notice No. 50, dated July 26, 2001.

The hand held barcode reader is a Class II laser device compliant with EN

60825-1:1994 + A2:2001.

Electromagnetic Conformity for “Industrial, Scientific and Medical” (ISM)

equipment, Group I, Class A:

• EMC Directive 89/336/EEC (European Union)

• CISPR 11: 1998 Industrial, Scientific and Medical (ISM) Radio-Frequency

Equipment - Radio disturbance characteristics - Limits and methods of

measurement

• EN 61326: 1997 Electrical equipment for measurement, control and

laboratory use – EMC Requirements

• EN 61000-4-2:1998 Electrostatic Discharge Immunity Test

• EN 61000-4-3:1996 Radiated Radio-Frequency

Electromagnetic Immunity Test

• EN 61000-4-4:1995 Electrical fast Transient/Burst Immunity

Test

• EN 61000-4-5:1996 Surge Immunity Test

• EN 61000-4-6:1996 Immunity to Conducted Disturbances,

induced by Radio-Frequency Fields

• EN 61000-4-11:1994 Voltage Dips and Interruptions

• EN 61000-3-2: 2000 Limit for Harmonic Current Emissions

chapter 1 | Regulatory Compliance 17

• EN 61000-3-3: 1995 Limit of Voltage fluctuations and Flicker

FCC Part 15 for Class A Equipment: This device complies with Part 15 of FCC

Rules. Operation is subject to the following two conditions: (1) This device

may not cause harmful interference, and (2) This device must accept any

interference received, including interference that may cause undesired

operation.

This Class A digital apparatus meets all requirements of the Canadian

Interference-Causing Equipment Regulation.

Cet appareil numérique de la classe A respecte toutes les exigences du

Règlement sur le matériel broullier du Canada.

Affymetrix complies with EU Directive 2002/96/EC (WEEE). In territories

with electrical equipment recycling mandates in effect, please contact your

Affymetrix representative for instructions on instrument disposal (Table 1.2).

Table 1.2

Regulatory compliance

18 GeneChip® HT Scanner User’s Guide

Technical Support

Affymetrix provides technical support to all licensed users via phone or E-mail. To

contact Affymetrix® Technical Support:

Design Elements and Specifications

ILLUMINATION SYSTEM

Light Source

The scanner uses a 300W xenon arc lamp as its light source. The lamp has a

lifetime of at least three hundred hours. The workstation software monitors the

on-time of the lamp so that you can be informed when the lamp is nearing end-

of-life. You can replace the lamp without the need for special tools or

alignment.

Affymetrix, Inc.

3380 Central Expressway

Santa Clara, CA 95051 USA

Tel: 1-888-362-2447 (1-888-DNA-CHIP)

Fax: 1-408-731-5441

support@affymetrix.com

Affymetrix UK Ltd.,

Voyager, Mercury Park,

Wycombe Lane, Wooburn Green,

High Wycombe HP10 0HH

United Kingdom

UK and Others Tel: +44 (0) 1628 552550

France Tel: 0800919505

Germany Tel: 01803001334

Fax: +44 (0) 1628 552585

supporteurope@affymetrix.com

[email protected]

Affymetrix Japan, K. K.

Mita NN Bldg

16 Floor, 4-1-23 Shiba,

Minato-ku, Tokyo 108-0014

Japan

Tel: (03) 5730-8200

Fax: (03) 5730-8201

www.affymetrix.com

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Thermo Fisher Scientific HT Scanner User guide

Thermo Fisher Scientific HT Scanner User guide

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