Troubleshoot Luminex Transform Scripts and Curve Fit Results

Documentation

This page provides tips on interpreting and fixing error messages from Luminex transform scripts. In addition, it includes troubleshooting advice for issues you may encounter when reviewing assay data and calculated values output from such scripts.

Transform Script Upload Errors

"An error occurred when running the script [script-filename.R] (exit code: 1)"

  • This message indicates that an error has occurred in the R transform script and has halted the script execution. In most case, if you look further down in the upload log file, you will see the details of the actual R error message.

"Error in library(xtable) : there is no package called 'xtable' - Calls: source -> withVisible -> eval -> eval -> library - Execution halted"

  • The named library cannot be located. You may need to download an additional package or check that your downloaded packages are in the R library directory. If you are using the R graphical user interface on Windows, you may need to hand copy the downloaded packages from a temp directory into the R/library directory. See the R documentation for more information about troubleshooting R in Windows.

"Error in plot.window(...) : need finite 'xlim' values"

  • This error message is usually the result of a problem in the Ruminex package when Ruminex tries to plot a curve fit PDF and encounters an x-axis or y-axis min/max value that is Infinity or Negative Infinity (for example, as a result of taking the log of a zero value). Check to see if you have zero values in the Expected Concentration column for one of your titrated standards.

"Illegal argument (4) to SQL Statement: NaN is not a valid parameter"
"Zero values not allowed in dose (i.e. ExpConc/Dilution) for Trapezoidal AUC calculation"

  • When the server attempts to calculate the area under the curve value for each for the selected titrations using the trapezoidal method, it uses the log of the ExpConc or Diliution values. For this reason, zero values are not allowed in either of these columns for the titrations that will have an AUC calculated.

"ERROR: For input string: 1.#INFE+000"

  • There is at least one bad value in the uploaded Excel file.  That value cannot be properly parsed for the expected field type (i.e. number). 

"NAs are not allowed in subscripted assignments"

  • This error has already been fixed to give a better error message. This error is an indication that values in the ExpConc column for some of the wells do not match between Analyte tabs of the Excel file. Verify that the ExpConc and Dilution values are the same across analytes for each of your well groups. Missing descriptions in control wells can also cause this error.

"Error in Ops.factor(analyte.data$Name, analytePtids$name[index])"

  • This error message indicates that there is a mis-match between the analyte name on the Excel file worksheet tab and the analyte name in the worksheet content (i.e. header and analyte column). Check that the bead number is the same for both.

Issues with uploaded results, curve fit calculations, plots, etc.

Missing values for AUC or EC50

  • When a curve fit QC metric (such as AUC or EC50) is blank for a given analyte, there are a few reasons that could be the cause (most of which are expected):
    • Check the curve fit's failure flag to make sure the parameters weren't out of range (e.g. 'AnalyteTitration/FiveParameterCurveFit/FailureFlag')
    • Check to see if Max(FI) of the curve fit points are less than 1000 - in which case the curve fit won't be run
    • Check to make sure that the AUC column being displayed is from the 'Trapezoidal Curve Fit' method and EC50 column is from the 'Five Parameter' or 'Four Parameter' fit method
    • Was the titration selected as QC Control or Standard on upload? (Check 'Well Role' column)

Levey-Jennings report showing too many or too few points on the default graph

  • The default Levey-Jennings report will show the last 30 uploaded results for the selected graph parameters. You can set your desired run date range using the controls above the graph to view more/less records.

Levey-Jennings Comparison plots and/or Curve Fit PDF plots showing curves sloping in different directions

  • QC Control titrations are plotted with dilution as the x-axis whereas Standard titrations are plotted with expected concentration on the x-axis. Make sure that your titrations were correctly set as either a QC Control or Standard on the well-role definition section of the Luminex upload wizard.

Incorrect positivity calls

  • When you encounter an unexpected or incorrect positivity call value, there are a few things to check:
    • Check that the Visit values are parsing correctly from the description field by looking at the following columns of the imported assay results: Specimen ID, Participant ID, Visit ID, Date, and Extra Specimen Info
    • Check that the run settings for the positivity calculation are as expected for the following fields: Calculate Positivity, Baseline Visit, and Positivity Fold Change
    • When the "Calculate Positivity" run property is set, the Analyte properties section will contain input fields for the "Positivity Thresholds" for each analyte. Check to make sure those values were entered correctly
    • Positivity calls for titrated unknowns will be made using only the data for the lowest dilution of the titration

 

Discussion

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