Luminex® analysis in LabKey Server makes use of a transform script to do a number of calculations including curve fits and estimated concentrations. To get the transform script running, you will need to:

• Install and Configure R if you have not already done so.
• Install Necessary Packages.
• Associate the Transform Script with the Assay Design.
• Test Package Configuration if you wish.

Install and Configure R

You will need to install R and configure it as a scripting language on your LabKey Server. If you are on a Windows machine, install R in a directory that does not contain a space (i.e. not the default "C:\Program Files\R" location).

Install Necessary R Packages

The instructions in this section describe package installation using the R graphical user interface.

Install Ruminex

The transform script requires Ruminex, a custom package not available on CRAN, so you will need to use the zip package provided in the sample files you downloaded. This tutorial was tested using Ruminex 0.1.0 (and 0.0.9); other versions may not work identically.

Install Additional Packages

install.packages("Rlabkey", repos="http://cran.rstudio.com")

Associate the Transform Script with the Assay Design

Control Access to Scripts

Next, place the transform script and utility script in a server-accessible, protected location.

Your script was uploaded into the Files web part earlier; however, we do not recommend running it from this location. If you do so, all users with edit-level permissions on your server will be able to replace/edit the script which runs with very high levels of permission on your server. Before continuing, place a copy of the transform script and its associated utility script in a safer location on your server. If your server runs on Windows, for example:

For more information about locating R scripts, see Transformation Scripts in R.

Add Path to Assay Design

Edit the transform script path in the assay design we provided to point to this location.

• In the Assay List of your Luminex folder, click Luminex Assay 200.
• Click Manage Assay Design > Edit assay design.
• In the Assay Properties section, for the Transform Script, enter the full path to the scripts you just placed.

• Click Save

When you save, the server will verify the script location.

Test Package Configuration

This step is optional, but will confirm that your R script will run as needed in the following tutorial steps.

• Click Luminex.
• In the Files web part, select /Luminex/Runs - Assay 200/02-14A22-IgA-Biotin.xls.
• Click Import Data.

• Select Use Luminex Assay 200 in the popup and click Import again.
• For Batch properties, leave defaults unchanged and click Next.
• For Run Properties, leave defaults unchanged and click Next.
• Click Save and Finish.

If there is a problem with the path, or with installed packages or the version of R, error messages will help you figure out what else you need to do (e.g., installing an additional R package or upgrading your version of R). After installing a missing package, you can refresh your browser window to see if additional errors are generated.

If your script cannot find youtil.R, make sure it is located in the same directory as the LabKey Luminex transform script. The following should be peers:

• labkey_luminex_transform.R
• youtil.R

When you see the Luminex Assay 200 Runs grid, you know your script was successfully run while importing the test run.

Delete the Imported Run Data

Before continuing with the tutorial, you need to delete the run you used to test your R configuration.

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