Applied Biosystems 7900HT Fast Real-Time PCR System and SDS ...

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Chapter 8TroubleshootingSoftware and 7900HT InstrumentTroubleshootingSoftware andComputerProblemsTable 8-4Troubleshooting Software and Computer ProblemsObservation Possible Cause Recommended ActionUnable to finish installation(Install program appears tobe frozen)Installer dialog box ishidden from view1. Press and hold Alt.2. Press Tab until the Installericon is selected.3. Release both keys.The installer dialog box returnsto the front of the desktop.SDS Software version 2.2does not function after theinstallation of SDS Softwareversion 2.2.1SDS software will not startThe software crashes/freezesthe computer or displays anerror messageSDS Software version2.2 is automaticallyremoved during theinstallation• Incorrect start-upsequence• Corrupted software• Computerhardware failure• Operating System(OS) corruption• Loose bar codereader cableReinstall the SDS Softwareversion 2.2Follow the solutions listed untilthe symptom goes away.1. Power off the 7900HTinstrument.2. Check cable connections.3. Restart the computer andlogon to the computer.4. Power on the 7900HTinstrument.5. Start the SDS software.6. Restart the computer andlogon to your computer.7. Reinstall the SDS software.8. Start the SDS software.123Contact Applied BiosystemsService for OS problems or ifthe computer will not boot up atall. You may have to reload theOS from the CDs.4Contact Dell for troubleshootingthe computer hardware.8-14 Applied Biosystems 7900HT Fast Real-Time PCR System and SDS Enterprise Database User GuideDRAFTSeptember 1, 2004 11:39 am, CH_Trouble.fm
Software and 7900HT InstrumentTable 8-4Troubleshooting Software and Computer ProblemsObservation Possible Cause Recommended ActionCommunication errorThermal cycler errorsAutomation ControllerSoftware cannot find a platedocument fileDialog box does not respondto mouse clicks or keystrokesCables are connectedincorrectlySample block modulenot fully engagedFile not in correctlocationJava Runtime ErrorCheck cable connections andCOM port setup. See“Instrument Connections” onpage 1-10.Reseat the sample blockmodule as explained“Replacing the Sample Block”on page 7-6.Remove file entry from platequeue and add the file to theplate queue again.Click the close box of the dialogbox to close it.Run will not start No calibration file Perform background and puredye runs.No background data inSee “Performing a Backgroundcalibration fileRun” on page 7-16 and(background run has“Performing a Pure Dye Run”not been performed)on page 7-20.No pure dye data incalibration file(pure dye run has notbeen performed)Calibration file doesnot contain pure dyedata for a dye used onthe plate documentCalibration file wascreated on anotherinstrumentDisk drive containingthe plate documenthas less than 50 MB offree spaceHeated cover cannotreach runningtemperature becauseno plate loadedCheck the capacity of thedestination drive. If less than50 MB of free space remains,remove or archive existing datafiles (see page 7-54).Open the instrument tray andcheck that the instrumentcontains a plate.Instrument traycontains a plateOutput stack containsa plate or platesRemove all plates from theoutput stack of the PlateHandler before starting thequeue.Applied Biosystems 7900HT Fast Real-Time PCR System and SDS Enterprise Database User Guide 8-15DRAFTSeptember 1, 2004 11:39 am, CH_Trouble.fm
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Applied Biosystems7900HT Fast Real-
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ContentsPrefaceHow to Use This Guid
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Chapter 4Operating the InstrumentNo
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Chapter 7Maintaining the Instrument
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Appendix D Theory of OperationFluor
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PrefaceHow to Use This GuidePurpose
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Safety and EMC Compliance Informati
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Symbols on InstrumentsSymbols on In
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General Instrument SafetyGeneral In
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Chemical Waste SafetyChemical Safet
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Physical Hazard SafetyOvervoltageRa
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Workstation SafetyWorkstation Safet
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Product Overview 11In This Chapter
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7900HT FAST Real-Time PCR SystemSec
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7900HT InstrumentInterchangeableThe
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7900HT FAST Real-Time PCR SystemBar
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Compatible ConsumablesCompatible Co
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Instrument ConnectionsFixed-Positio
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Section 1.2 Getting to Know the Sof
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SDS Software Related Files and Form
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7900HT FAST Real-Time PCR SystemMan
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Esc F1 F2 F3 F4 F5 F6 F7 F8 F9 F10
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Section 1.3 SDS Enterprise Database
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* + Enter* +Enter3Down UpNumLockSys
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About the SDS Enterprise Database S
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Esc F1 F2 F3 F4 F5 F6 F7 F8 F9 F10
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Getting Started 22In This Chapter G
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Getting StartedUsing the SDSSoftwar
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GR23967900HTPowering On the 7900HT
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Using the SDS SoftwareUsing the SDS
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Using the SDS SoftwareAbout theMess
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Basic Software Skills TutorialNotes
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Basic Software Skills TutorialExerc
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Basic Software Skills TutorialExpor
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Basic Software Skills TutorialLesso
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Basic Software Skills Tutorial3. Se
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Using SDS Plate DocumentsUsing SDS
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Using SDS Plate DocumentsWell Inspe
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Preparing a Run 33In This Chapter N
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Notes for Database UsersDescription
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Workflow OverviewWorkflow OverviewE
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Workflow OverviewAllelicDiscriminat
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Step 1 - Creating a Plate DocumentS
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Step 2 - Applying Detectors and Mar
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Step 3 - Configuring the Plate Docu
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Step 5 - Programming the Plate Docu
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Step 6 - Saving the Plate Document
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Step 7 - Creating a Plate Document
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Step 9 - Running the Plate on the 7
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Operating the Instrument 44In This
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Section 4.1 Consumable PreparationS
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Compatible ConsumablesTable 4-1Comp
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Preparing Optical Plates for Usea.
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Preparing TaqMan Low Density Arrays
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Section 4.2 Running an Individual P
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Running a Single Plate (Using the S
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Running a Single Plate (Using the S
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After the RunAfter the RunUser Acce
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Section 4.3 Automated OperationSect
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Operating the Software with an SDS
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Operating the Software without an S
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Running Plates Using the Automation
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Running Plates Using the Automation
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Analyzing End-Point Data 55In This
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Notes for Database UsersNotes for D
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Section 5.1 Allelic DiscriminationS
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OverviewTable 5-1Signal and Sequenc
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Before You BeginBefore You BeginUsi
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Opening the Run DataOpening the Run
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Calling and Scrutinizing Allelic Di
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After the AnalysisSaving theResults
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Analyzing Real-Time Data 66In This
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Section 6.1 Absolute Quantification
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OverviewAlgorithmicManipulation ofR
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Analysis ChecklistAnalysis Checklis
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Analyzing the DataAnalyzing the Dat
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Viewing ResultsViewing ResultsViewi
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Section 6.2 Relative Quantification
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OverviewAlgorithmic Manipulation of
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OverviewAutomatic Outlier RemovalAb
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Getting StartedGetting StartedUsing
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Options for Analyzing Relative Quan
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Creating the Studyd. In the Plate Q
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Analyzing the Study• Manual Ct -
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Analyzing the StudySpecifying the A
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Viewing ResultsViewing ResultsDispl
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Viewing ResultsAbout DownArrowsDown
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After the AnalysisAfter the Analysi
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Section 6.3 Dissociation Curve Anal
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Before You BeginExample ResultsFigu
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Opening the Run DataOpening the Run
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Determining T m Values for the Anal
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Section 6.4 Procedure ReferenceSect
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Setting the Baseline and Threshold
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Eliminating Outlying AmplificationE
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Eliminating Outlying Amplification6
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After the AnalysisSaving theResults
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Maintaining the Instrument 77In Thi
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Section 7.1 Maintaining the 7900HT
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Replacing the Sample BlockMaterials
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Replacing the Sample Block9. Loosen
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7900HT FAST Real-Time PCR SystemRep
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Changing the Plate Adapter4. Place
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Decontaminating the Sample BlockCle
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Performing a Background RunPreparin
Page 251 and 252: Performing a Background RunAnalyzin
Page 253 and 254: Performing a Pure Dye RunAfter a ru
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Page 257 and 258: Performing a Pure Dye RunAnalyzing
Page 259 and 260: Adding Custom Dyes to the Pure Dye
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Page 263 and 264: Verifying Instrument PerformanceTab
Page 265 and 266: Verifying Instrument PerformancePre
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Page 269 and 270: Adjusting the Sensitivity of the Pl
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Page 275 and 276: Aligning the Plate Handler5. Using
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Page 283 and 284: Aligning the Fixed-Position Bar Cod
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Page 287 and 288: Maintaining the SDS softwareSeveral
Page 289 and 290: Troubleshooting 88In This Chapter T
Page 291 and 292: Troubleshooting TableTable 8-1Troub
Page 293 and 294: Low Precision or IrreproducibilityL
Page 295 and 296: Low Precision or IrreproducibilityD
Page 297 and 298: Background RunsBackground RunsBackg
Page 299 and 300: Pure Dye Runs6. Repeat step 4 until
Page 301: End-Point Runs (Allelic Discriminat
Page 305 and 306: Zymark Twister Microplate Handler a
Page 307 and 308: TaqMan Low Density ArrayTable 8-6Tr
Page 309 and 310: Software ReferenceAAIn This Appendi
Page 311 and 312: Importing Plate Document Setup Tabl
Page 313 and 314: Setup Table Files1. File VersionDes
Page 315 and 316: Setup Table Files6. Detectors ListD
Page 317 and 318: Setup Table Files9. Markers List (A
Page 319 and 320: Setup Table FilesFormat(for a singl
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Page 323 and 324: Setup Table FilesExample Code A-16A
Page 325 and 326: Exporting Plate Document Data4. In
Page 327 and 328: Operating the SDS Software from a C
Page 329 and 330: Using the Search ToolLogical Operat
Page 331 and 332: Connecting SDS Software to the Data
Page 333 and 334: Designing TaqMan Reagent-BasedAssay
Page 335 and 336: Assay Development Guidelines• For
Page 337 and 338: Design Tips for Allelic Discriminat
Page 339 and 340: Kits, Reagents, and ConsumablesCCIn
Page 341 and 342: Consumables and DisposablesConsumab
Page 343 and 344: Instrument Maintenance and Verifica
Page 345 and 346: Custom Oligonucleotide SynthesisTab
Page 347 and 348: Theory of OperationDDIn This Append
Page 349 and 350: Fluorescent-Based ChemistriesBasics
Page 351 and 352: Real-Time Data AnalysisPhase 2: Lin
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Real-Time Data AnalysisSignificance
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A similar equation for the endogeno
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Limited Warranty StatementEEWarrant
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BibliographyGeneral Paperson TaqMan
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Klein, D., Janda, P., Steinborn, R.
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Dolken, L., F. , Schuler, and G. ,
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AllelicDiscriminationVirtanen M., H
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Glossary.sdd.sdm.sds.sdt∆C T∆
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ackgroundbaselinecalibratorcDNA(com
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minor groovebinder (MGB)multicompon
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R nrunsessionsingle nucleotidepolym
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IndexSymbols- 6-31↑ 6-33Numerics7
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fluorescent, common sources 8-7isol
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adjusting step parameters 3-21confi
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sample block locking bar 7-8sample
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Worldwide Sales and SupportApplied
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