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.
| Name | Label | Type | Description |
| TransformVersion | Transform Script Version | Text (String) | Version number of the transform script (to be populated by the transform script) |
| RuminexVersion | Ruminex Version | Text (String) | Version number of the Ruminex R package (to be populated by transform script |
| Name | Label | Type | Description |
| SubtNegativeFromAll | Subtract Negative Bead from All Wells | Boolean | Controls 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. |
| StndCurveFitInput | Standards/Controls FI Source Column | Text (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). |
| UnkCurveFitInput | Unknowns FI Source Column | Text (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). |
| CurveFitLogTransform | Curve Fit Log Transform | Boolean | Whether 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. |
| NotebookNo | Notebook Number | Text (String) | Notebook number |
| AssayType | Assay Type | Text (String) lookup | Lookup into lists.AssayType |
| ExpPerformer | Experiment Performer | Text (String) | Who performed the experiment |
| CalculatePositivity | Calculate Positivity | Boolean | Whether or not the calculate the positivity for this run |
| BaseVisit | Baseline Visit | Number (Double) | The baseline visit for positivity calculations |
| PositivityFoldChange | Positivity Fold Change | Number (Integer) - lookup with 3x and 5x | Fold change used to determine positivity |
| SkipRumiCalculation | Skip Rumi Calculation | Boolean | Set to true to allow calculation of 4PL EC50 and AUC on upload without running the Ruminex calculation |
| Name | Label | Type | Description |
| FileName | File Name | Text (String) | The file name |
| AcquisitionDate | Acquisition Date | DateTime | |
| ReaderSerialNumber | Reader Serial Number | Text (String) | |
| PlateID | Plate ID | Text (String) | |
| RP1PMTvolts | RP1 PMT (Volts) | Number (Double) | |
| RP1Target | RP1 Target | Text (String) |
| Name | Label | Type | Description |
| LotNumber | Lot Number | Text (String) | The lot number for a given analyte |
| NegativeControl | Negative Control | Boolean | Indicates which analytes are to be treated as negative controls (i.e. skip curve fit calculations, etc.) |
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.
| Name | Label | Type | Description |
| FIBackgroundNegative | FI-Bkgd-Neg | Number (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 |
| Standard | Standard for Rumi Calc | Text (String) | The name of the standard used for the transform script estimated concentration calculations based on the rumi curve fits |
| EstLogConc_5pl | Est Log Conc Rumi 5 PL | Number (Double) | The transform script calculated estimated log concentration value using a 5PL curve fit |
| EstConc_5pl | Est Conc Rumi 5 PL | Number (Double) | The transform script calculated estimated concentration value using a 5PL curve fit |
| SE_5pl | SE Rumi 5 PL | Number (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 |
| Positivity | Positivity | Text (String) | The transform script calculated positivity value for unknowns |
| Slope_4pl | Slope Param 4 PL | Number (Double) | Optional. The transform script calculated slope parameter of the 4PL curve fit for a given analyte/titration |
| Lower_4pl | Lower Param 4 PL | Number (Double) | Optional. The transform script calculated lower/min parameter of the 4PL curve fit for a given analyte/titration |
| Upper_4pl | Upper Param 4 PL | Number (Double) | Optional. The transform script calculated upper/max parameter of the 4PL curve fit for a given analyte/titration |
| Inflection_4pl | Inflection Param 4 PL | Number (Double) | Optional. The transform script calculated inflection parameter of the 4PL curve fit for a given analyte/titration |
| Slope_5pl | Slope Param 5 PL | Number (Double) | Optional. The transform script calculated slope parameter of the 5PL curve fit for a given analyte/titration |
| Lower_5pl | Lower Param 5 PL | Number (Double) | Optional. The transform script calculated lower/min parameter of the 5PL curve fit for a given analyte/titration |
| Upper_5pl | Upper Param 5 PL | Number (Double) | Optional. The transform script calculated upper/max parameter of the 5PL curve fit for a given analyte/titration |
| Inflection_5pl | Inflection Param 5 PL | Number (Double) | Optional. The transform script calculated inflection parameter of the 5PL curve fit for a given analyte/titration |
| Asymmetry_5pl | Asymmetry Param 5 PL | Number (Double) | Optional. The transform script calculated asymmetry parameter of the 5PL curve fit for a given analyte/titration |
| previousnext |
| expand allcollapse all |
