Custom Assay Fields for LabKey Luminex Transform Script

To set up a Luminex assay to run the LabKey Luminex transform script used in the Luminex Assay Tutorial Level II, you need to include certain custom fields in the assay design.  The script outputs results into these fields.  This page provides details on these output fields.  Labs may add additional, lab-specific fields when convenient, but only the fields below are used by the Ruminex transform script.

For reference, the fields included by default in a Luminex assay design are listed on the Luminex Properties page.

Appendix A: Custom Batch Fields

NameLabelTypeDescription
TransformVersionTransform Script VersionText (String)Version number of the transform script (to be populated by the transform script)
RuminexVersionRuminex VersionText (String)Version number of the Ruminex R package (to be populated by transform script

Appendix B: Custom Run Fields

NameLabelTypeDescription
SubtNegativeFromAllSubtract Negative Bead from All WellsBooleanControls whether or not the negative bead values should be subtracted from all wells or just the unknowns. Values for the negative bead for each run are reported on the Negative (Bead Number) tab of the run's Excel file.
StndCurveFitInputStandards/Controls FI Source ColumnText (String)The source column to be used by the transform script for the analyte/titration curve fit calculations of Standards and QC Controls (if lookup configured, choices include: FI, FI-Bkgd, and FI-Bkgd-Neg).
UnkCurveFitInputUnknowns FI Source ColumnText (String)The input source column to be used by the transform script when calculating the estimated concentration values for non-standards (if lookup configured, choices include: FI, FI-Bkgd, and FI-Bkgd-Neg).
CurveFitLogTransformCurve Fit Log TransformBooleanWhether or not to take the log transform of the FI data for the curve fits. When set to true, FI (minus any chosen background subtractions for background wells or negative beads) is log transformed before calculation of curve fit regression parameters and interpolation of unknowns from the curve.
NotebookNoNotebook NumberText (String)Notebook number
AssayTypeAssay TypeText (String) lookup Lookup into lists.AssayType
ExpPerformerExperiment PerformerText (String) Who performed the experiment
CalculatePositivityCalculate PositivityBooleanWhether or not the calculate the positivity for this run
BaseVisitBaseline VisitNumber (Double)The baseline visit for positivity calculations
PositivityFoldChangePositivity Fold ChangeNumber (Integer) - lookup with 3x and 5xFold change used to determine positivity
SkipRumiCalculationSkip Rumi CalculationBooleanSet to true to allow calculation of 4PL EC50 and AUC on upload without running the Ruminex calculation

Appendix C: Custom Excel File Run Properties

NameLabelTypeDescription
FileNameFile NameText (String)The file name
AcquisitionDateAcquisition DateDateTime 
ReaderSerialNumberReader Serial NumberText (String) 
PlateIDPlate IDText (String) 
RP1PMTvoltsRP1 PMT (Volts)Number (Double) 
RP1TargetRP1 TargetText (String) 

Appendix D: Custom Analyte Properties

NameLabelTypeDescription
LotNumberLot NumberText (String)The lot number for a given analyte
NegativeControlNegative ControlBooleanIndicates which analytes are to be treated as negative controls (i.e. skip curve fit calculations, etc.)

Appendix E: Custom Data Fields

The optional fields in this section are not required for the Ruminex script to run.  They are specific curve fit parameters returned by the transform script. They may be useful to statisticians.

NameLabelTypeDescription
FIBackgroundNegativeFI-Bkgd-NegNumber (Double)The value calculated by the transform script by subtracting the FI-Bkgd of the negative bead from the FI-Bkgd of the given analyte bead
StandardStandard for Rumi CalcText (String)The name of the standard used for the transform script estimated concentration calculations based on the rumi curve fits
EstLogConc_5plEst Log Conc Rumi 5 PLNumber (Double)The transform script calculated estimated log concentration value using a 5PL curve fit
EstConc_5plEst Conc Rumi 5 PLNumber (Double)The transform script calculated estimated concentration value using a 5PL curve fit
SE_5plSE Rumi 5 PLNumber (Double)The transform script calculated standard error value using a 5PL curve fit

EstLogConc_4pl

Est Log Conc Rumi 4 PL

Number (Double)The transform script calculated estimated log concentration value using a 4PL curve fit

EstConc_4pl

Est Conc Rumi 4 PL

Number (Double)The transform script calculated estimated concentration value using a 4PL curve fit

SE_4pl

SE Rumi 4 PL

Number (Double)The transform script calculated standard error value using a 4PL curve fit
PositivityPositivityText (String)The transform script calculated positivity value for unknowns
Slope_4plSlope Param 4 PLNumber (Double)Optional. The transform script calculated slope parameter of the 4PL curve fit for a given analyte/titration
Lower_4plLower Param 4 PLNumber (Double)Optional. The transform script calculated lower/min parameter of the 4PL curve fit for a given analyte/titration
Upper_4plUpper Param 4 PLNumber (Double)Optional. The transform script calculated upper/max parameter of the 4PL curve fit for a given analyte/titration
Inflection_4plInflection Param 4 PLNumber (Double)Optional. The transform script calculated inflection parameter of the 4PL curve fit for a given analyte/titration
Slope_5plSlope Param 5 PLNumber (Double)Optional. The transform script calculated slope parameter of the 5PL curve fit for a given analyte/titration
Lower_5plLower Param 5 PLNumber (Double)Optional. The transform script calculated lower/min parameter of the 5PL curve fit for a given analyte/titration
Upper_5plUpper Param 5 PLNumber (Double)Optional. The transform script calculated upper/max parameter of the 5PL curve fit for a given analyte/titration
Inflection_5plInflection Param 5 PLNumber (Double)Optional. The transform script calculated inflection parameter of the 5PL curve fit for a given analyte/titration
Asymmetry_5plAsymmetry Param 5 PLNumber (Double)Optional. The transform script calculated asymmetry parameter of the 5PL curve fit for a given analyte/titration

Discussion

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