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LabChip GX
PerkinElmer LabChip GX User Manual
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Data Analysis
64
V4.2
LabChip GX User Manual
PerkinElmer
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Table of Contents
Preface
2
Instrument Safety
7
Required Training
7
Chemical Safety
8
Laser Safety
9
Electrical Safety
10
Power Cord Selection
10
Fuses
11
Mechanical Safety
11
Table of Contents
12
Introduction
18
Principles of Operation
19
Software Modes Available
21
Operation
22
Opening the Labchip GX Software
23
Creating Desktop Shortcuts
23
Creating a New Assay
24
Running an Assay
25
Select the Auto Export Settings
29
Monitoring the Run
30
Stopping a Run
31
Continuing a Stopped Run
32
Saving Data Files
33
Saving Workspace Files
34
Selecting Wells Using a Sample Names File
35
Using a Barcode to Specify the Sample Names File
36
Adding a New Plate
38
Placing the Barcode on the Plate
40
Calibrating the Optics
41
Data Analysis
42
How the Software Analyzes DNA Data
43
How the Software Analyzes Protein Data
45
How the Software Analyzes RNA Data
49
How the Software Analyzes Glycan Data
54
How the Software Analyzes Protein Charge Variant Data
57
How the Software Analyzes Genomic DNA Data
58
Organizing, Retrieving, and Backing up Data Files
59
Opening a New Workspace
59
Opening a Data File
60
Adding a Collection to a Workspace
61
Selecting the Wells in a Collection
62
Using Sample Names Files
63
Create a Sample Name File
63
Sample Name File Format (.CSV Format)
65
Applying Different Window Values to Expected Peaks of the same Size in Different Wells
66
Sample Name File Import Errors
66
Using Expected Fragments/ Expected Proteins/Expected Glycans
67
Entering Efs, Eps, or Egs in the Assay Analysis Window
67
Exporting Efs, Eps, or Egs
68
Importing Efs, Eps, or Egs
68
Forcing Expected Peaks
69
Viewing the Efs/Eps/Egs in the Graph View
69
Viewing the Efs/Eps/Egs in the Gel View
70
Viewing the Efs/Eps/Egs in the Well Table
71
Viewing the Efs/Eps/Egs in the Peak Table
71
Modifying Analysis Parameters
72
Changing the Peak Find Parameters
73
Adding a Peak
74
Excluding a Peak
74
Splitting a Peak
75
Merging Two Peaks
75
Adjusting the Peak Baseline
76
Setting the Baseline for a Range of Peaks
76
Removing a Manual Baseline
77
Selecting a Default Ladder
77
Using the Default Ladder for Alignment
79
Exporting the Default Ladder in an Assay
79
Clearing the Default Ladder in a Plate
79
Changing the Time Window for Analysis
80
Aligning or Unaligning the Marker Peaks
80
Saving and Exporting Assays
84
Changing the View of the Data
85
Viewing Gels
85
Viewing Zero Baselines
86
Adjust Pane Widths
87
Show or Hide Views
87
Zoom in and Zoom out
88
Viewing Graphs in the Overlay Electropherograms Tab
89
Viewing Graphs in the Electropherograms Tab
90
Viewing Analysis Errors and Warnings
92
Viewing Multiple Properties in the Well Table View
93
Copying Information
94
Reanalyzing a Data File
95
Printing Workspace Information
96
Exporting Data
102
Exporting Data Manually
105
Using the GX Software to Analyze GX Touch Data
107
Understanding Peak Finding
108
Data Smoothing
108
Peak Detection - Slope Threshold
109
Peak Splitting - Inflection Threshold
112
Peak Identification
113
Software Security
114
Locking and Unlocking the Software
116
Managing User Accounts
117
Adding New Users
118
Changing User Information
119
Printing User Information
120
Activating and Deactivating User Accounts
120
Changing Access Rights
121
Printing Access Rights
122
Setting Policies for User Accounts
123
Printing User Policies
124
Electronic Signatures
125
Automatically Exporting Copies of Data Files
126
Reverting to a Specific Data File Revision
126
Audit Trail
127
Viewing the Audit Trail
128
Exporting the Audit Trail
129
Central Data Repository (CDR)
130
CDR Security Suggestions
130
Creating New Data Folders
131
Moving Data Files into Folders
131
Deleting Data Folders
131
Hiding Data Files in the CDR Manager Window
132
Showing Hidden Data Files in the CDR Manager Window
132
Remote CDR Server Backup
133
Setting up the Remote CDR Server
133
Backing up Data Files to the Remote CDR
135
Restoring Data Files from the Remote CDR
136
Viewing the Files in the Remote CDR Folder
137
Manually Backing up and Restoring the CFR Files
138
Backing up CFR Files
138
Restoring CFR Files
140
Software Reference
142
Labchip GX Main Window
143
Menu Bar
144
Chip Status and Run Status
151
Error Message Area
153
Plate View or Plate List
154
Collection Pane
157
Graph View
158
Graph View Properties
164
Gel View
167
Gel View Properties
170
Well Table View
172
Peak Table View
174
Peak Table Properties
179
Filter View
180
About Labchip GX Window
183
Add New Expected Peak Window
184
Add Plate Window
185
Assay Analysis Window
186
Assay Information Tab
187
Alignment Tab
188
Analysis Tab
189
Peak Find Tab
192
Expected Fragments/Proteins/Glycans Tab
196
Excluded Peaks Tab
198
Smear Analysis Tab
200
Titer Tab
202
Advanced Tab
205
Audit Trail Window
208
Audit Trail Export Window
209
Audit Trail Manage Columns Window
210
CDR Manager Window
211
CDR Server Utility Window
213
CDR Utility Window
214
Change Password Window
216
Data File Version Window
217
Event Viewer Window
218
Export Window
219
Installation Qualification Window
222
Layout Options Window
223
Login Window
224
New Collection Window
225
Optics Calibration Window
226
Perform Signature Window
228
Plate Information Window
229
Print Window
230
Print Validation Reports Window
232
Rename Collection Window
233
Robot Teaching Wizard
234
Welcome Window
235
Teach Robot Window
236
Teach the X, y and Z Reference Positions Window
237
Verify a Plate Window
238
Verify Positions Window
239
Finished Window
240
Verify All Target Positions Window
241
Verify All Target Positions Correct Window
242
Run File Editor Window
243
Run Info Window
244
Sample Name Editor Window
245
Save Workspace as Window
247
Select a Data File Window
248
Start Run Window
249
Run Tab
250
Output Tab
252
Advanced Tab
254
System Diagnostics Window
256
Unlock Application Window
258
Unlock Data File Window
259
User Administration Window
260
Create New User
261
Edit Users
263
Show User Info
264
De/Activate User
266
Define Access
267
Set Policies
269
Labchip GX Instrument Description
270
Front View
270
Front Panel
271
Rear Connectors
272
Optics
273
Chip Pressure System
273
Barcode Reader
273
DNA, RNA, and Protein Chips
274
Chip Cartridge
275
High Voltage Interface
276
Microplate Carrier
277
USB Key for 21 CFR Part 11 Option
277
Specifications
278
General
278
Environmental
278
Electrical
278
Assay Voltage
279
Chip Pressure
279
Chip Temperature Control
279
Fluorescence Detection
279
Light Source (Red Laser Diode)
279
Barcode Reader
279
Maintenance and Service
280
Cleaning the Chip Cartridge
281
Cleaning the Instrument Electrodes
281
Cleaning Test Chip C
282
Troubleshooting and Diagnostics
283
Searching for Events in the Events Tab
283
Viewing Current Events in the Events Tab
284
Viewing Past Events in the Events Tab
284
Error Messages
285
Device <Name> Is Disconnected
286
Plate Carrier Motion Blocked
286
Home Timeout
286
Move Timeout
287
Pressure Leak Detected
287
Focus Failed
287
Maximum Samples Exceeded
288
Chip Primed for Different Assay
288
HV Check Failed
288
Current Leakage Check Failed
289
Chip Temperature Warning
289
Running Installation Qualification (IQ)
290
Running Operational Qualification (OQ)
290
Diagnostics
291
Running the Diagnostics Tests
291
Description of Diagnostic Tests
292
Troubleshooting Assay Problems
298
Software Problems
298
Cannot Save a File
298
Computer Software Lock-Ups
299
Zipping the Log Files
300
Tips and Shortcuts
301
Glossary of Terms
302
Data Files
307
Perkinelmer Product Warranty
330
Perkinelmer Software License Agreement
332
Index
336
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PerkinElmer LabChip GX Specifications
General
Brand
PerkinElmer
Model
LabChip GX
Category
Measuring Instruments
Language
English
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