• Applied Biosystems Analysis Software Help
    • Getting started
    • Analysis workflow
    • System requirements
    • Compatible Real-Time PCR System Data
    • Applied Biosystems Software interface
    • Best practices and tips for using the software
  • Video library
    • Getting started with gene expression
    • Review data using the Outlier Wheel Plot
    • Calculations in relative quantitation
  • Manage your projects and experiment data
    • Create a project and add experiment data
    • Manage projects and experiment data
    • Share experiments, folders, and projects
    • Experiment data/files
  • Set up the project
    • Create or edit an analysis group
      • Version 1.1 algorithm improvements and settings
    • Manage samples and targets
    • Manage biological groups
    • Configure the analysis settings
    • Import sample information from design files
    • Import target information from AIF
    • Define endogenous controls for the analysis
  • Edit experiment properties
    • Review and edit the plate setups
    • Review the OpenArray QC images
    • Apply samples and targets
    • Specify and assign tasks
    • Specify and assign standards
    • Plate setup files
    • Use a plate setup file to apply plate layout information
  • Review the raw data
    • Review the quality data
    • Using the Amplification Plot Histogram
    • Amplification plot
    • Multicomponent plot
    • About the quality data summary
    • Omit wells from the analysis
  • Review the analyzed data
    • Review the analyzed data and plots
    • Box Plot
      • Change the Box Plot display
    • Correlation Plot
    • RQ plot
    • Heatmap Plot
    • Volcano Plot
      • View and modify the Volcano Plot
    • Melt Curve Plot
    • Omitting wells and samples
  • Export the results
    • Export the analyzed data from a project
    • Export project data as a slide presentation
    • Export plots for presentation and publication
    • Export data for use in other projects
  • Screens and plots
    • Amplification plot
    • Analysis screen
    • Box Plot
    • Correlation Plot
    • Data Review screen
    • Export screen
    • Heatmap Plot
    • Melt Curve Plot
    • Multicomponent plot
    • Outlier Wheel Plot
    • Overview screen
    • Plate Setup screen
    • RQ plot
    • Volcano Plot
    • Well Table
  • Error messages and troubleshooting
  • Quality flags
    • AMPNC flag (amplification in negative control)
    • AMPSCORE (Low signal in linear phase) quality flag
    • Amp Status (amplification status) value
    • BADROX flag (bad passive reference signal)
    • BLFAIL flag (Automatic Baseline Algorithm failed to identify baseline region)
    • CQCONF flag (calculated confidence in the Cq value is low)
    • CRTAMPLITUDE flag (low relative amplitude)
    • CRTNOISE flag (high relative noise)
    • CTFAIL flag (Baseline Threshold Algorithm failed to identify Ct)
    • DRNMIN flag (detection of minimum ∆Rn due to abnormal baseline)
    • EXPFAIL flag (Baseline Threshold Algorithm failed to identify exponential region)
    • HIGHSD flag (high standard deviation in replicate group)
    • LOWROX (Low ROX Intensity) quality flag
    • MAXCT (Cq above maximum) quality flag
    • MPOUTLIER (ΔCq outlier in multiplex experiment) quality flag
    • MTP flag (melt curve analysis shows more than one peak)
    • NOAMP flag (no amplification)
    • NOISE flag (noise is higher than other wells in plate)
    • NOSAMPLE (No sample assigned to well) quality flag
    • NOSIGNAL flag (no signal in well)
    • OFFSCALE flag (fluorescence signal is offscale)
    • OUTLIERRG flag (outlier detected in replicate group)
    • PRFDROP flag (passive reference signal changes significantly near the Cq)
    • PRFLOW flag (average passive reference signal is below the threshold)
    • SPIKE flag (noise spikes)
    • THOLDFAIL flag (Automatic Threshold Algorithm failed to identify threshold)
  • Documentation and support
    • Customer and technical support
    • Limited product warranty
  • Legal