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Customize Luminex Assay for Script

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Customize Luminex Assay for Script

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This topic details the minimal number of setup steps necessary to create a custom Luminex assay that works with the LabKey Luminex transform script. You can start from the default Luminex assay type that is built into the server, or as an alternative, it may be easier to start with the XAR-generated assay design used by the Luminex Assay Tutorial Level II and customize the design to your needs.

It may be helpful to use the Review Fields for Script page in addition to this topic.

Create a New Assay Design

These steps assume that you have already created a "Luminex" folder (of type "Assay"), as described in Setup Luminex Tutorial Project.

  • In the Assay List, click New Assay Design.
  • Choose the Luminex assay type.
  • At the bottom of the page, in the Assay Location, choose Current Folder. This is important to ensure that lookups to lists in the same folder will work.
  • Click Next.
  • Give the new assay design a Name.
  • Optional: Check the Import in Background box.
    • Checking this box means that assay imports will be processed as jobs in the data pipeline, which is helpful because Luminex runs can take a while to load.
  • Add fields as described in the following sections before clicking Save & Close.

Add Script-specific Fields

Make sure not to put a space in the Name property for any field you add. See Review Fields for Script page for details about each field.

The optional field property settings on tabs in the panel on the right can be used to customize field behavior. For example, you can prevent editing of particular values after a run has been imported in cases where those values are used for calculations/graphs during import. In this case we don't want the user inadvertantly changing the script version each time they run it.

Add Batch Fields

  • In the Batch Fields section, click the Add Field button for each of the following:
  • Add a field for TransformVersion:
    • Optional: On the display tab, uncheck the Shown in > Insert option (so that the user is not asked to enter a value).
    • Optional: On the advanced tab, change the Default Type to Fixed Value (so that you can specify a fixed value for the default for this field).
  • Add a field for RuminexVersion:
    • Optional: On the display tab, uncheck the Shown in > Insert option.
    • Optional: On the advanced tab, change the Default Type to Fixed Value.

Add Run Fields

  • In the Run Fields section:
  • Add a field for NotebookNo of type Text (String).
  • Add a field for SubtNegativeFromAll of type Boolean.
    • Optional: Uncheck the Update box on the display tab.
  • Add a field for StndCurveFitInput:
    • The type of this field can be either Text (String) or a lookup to a list which has the following three string values: FI, FI-Bkgd, FI-Bkgd-Neg.
    • Optional: Uncheck the Update box on the display tab.
    • Optional: based on the lab preference, you may want to set this field to either remember the last entered value or to have an editable default value selected (the script defaults to using the “FI” column if no value is specified for the StndCurveFitInput field). When creating this lookup and others, you may find it useful to import the list archive provided in the Setup Luminex Tutorial Project. If you import this archive of lists into the same folder as your assay, you can set this field to target the relevant list.
  • Add a field for UnkCurveFitInput:
    • The type of this field can be either Text (String) or a lookup to a list which has the following three string values: FI, FI-Bkgd, FI-Bkgd-Neg.
    • Optional: Uncheck the Update box on the display tab.
    • Optional: Based on the lab preference, you may want to set this field to either remember the last entered value or to have an editable default value selected (the script defaults to using the “FI” column if no value is specified for the UnkCurveFitInput field)
  • Add a field for CurveFitLogTransform of type Boolean.
  • Optional: Add a field for CalculatePositivity of type Boolean.
  • Optional: Add a field for BaseVisit of type Number (Double).
  • Optional: Add a field for PositivityFoldChange of type Number (Double).
  • Optional: If you would like users to be able to choose whether to skip Ruminex calculations, add a field for SkipRumiCalculation of type Boolean.

Add Analyte Properties

  • In the Analyte Properties section:
  • Add a field for LotNumber of type Text (String).
  • Optional: Add a field for NegativeControl of type Boolean.

Add Data Fields

  • In the Assay Data Fields section:
  • Add a field for FIBackgroundNegative of type Number (Double).
  • Add a field for Standard of type Text (String).
  • Add a field for EstLogConc_5pl of type Number (Double).
  • Add a field for EstConc_5pl of type Number (Double).
  • Add a field for SE_5pl of type Number (Double).
  • Add a field for EstLogConc_4pl of type Number (Double).
  • Add a field for EstConc_4pl of type Number (Double).
  • Add a field for SE_4pl of type Number (Double).
  • Optional: Add a field for Positivity of type Text (String).
  • Optional:
    • Add the optional Data Property fields listed in Appendix D. These are filled in by the transform script and may be interesting to statisticians.
Once all of the custom properties have been added to the assay design, click the Save & Close button.

Customize Data Grids

Any properties you add to the assay design can also be added to the various results, run, and batch grid views for the assay using the Grid Views > Customize Grid menu option.

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