LabKey Biologics offers a number of different ways to work with assay data in the system. Administrators can control which options are available and to which users.
Assay Data Dashboards
on the main menu to go to the assay dashboard. The default view is a grid listing the Assay Designs
in the system with names, descriptions, and types.
You can click the Grid
selector to choose a Heatmap
view instead, in which the available assay designs are rows and the last twelve months are columns. Color density indicates the amount of assay data that has been entered into the system. Clicking a cell in the heat map navigates to the data for the given assay type and month.
Assay Design Details
Click the name of an Assay Design to see it's summary page, with several tabs, showing various scopes of the data:
- Overview - Displays the name and description for the assay. A grid of runs is also shown.
- Batches (If defined) - View batches, the widest grouping of the data. Each batch generally groups together multiple runs of data.
- Runs - Displays run-level metadata about the assay results. Runs are the mid-level grouping of the data, standing between the batches and the result data. Each run generally represents one file of data.
- Results - Displays the result data of the assay, showing the data output of the instrument.
On assay data grids, any visualizations that have been added to the assay, can be seen by clicking the Charts
button. If the Charts button is grey-out, then no visualizations have been associated with the current assay at the selected scope. (Administrators can add charts to an assay, as detailed in the topic: Biologics Admin: Charts and Reports
Custom grid views are available by clicking the Grid Views
button. (Administrators can add custom data grids to an assay at any level, as detailed in the topic: Biologics Admin: Charts and Reports
Assay Quality Control
Visibility of assay data in Biologics can be controlled by setting quality control states. While an admin can edit assay designs to use QC states within the Biologics application, the actual states themselves cannot be configured in the application.
Set Up QC States (Admin)
To configure states, an admin must:
- Open the Assay Design where you want to use QC. Select > Edit Design.
- Confirm that the QC States checkbox is checked. If not, check it and click Finish Updating [Assay Design Name].
- Use > LabKey Server > [current Biologics project name] to switch interfaces.
- Configure the available QC states in the system, using this topic: Assay QC States - Admin Guide.
- Select (Admin) > Manage Assays.
- Click the name of your assay design.
- Select QC State > Manage states.
- Define the states you want to use.
- Once complete, use > LabKey Biologics > [current Biologics project name] to return to Biologics.
Use QC States (Users)
Once QC states have been configured in the system, users (with the appropriate roles) can assign those states to assay run data. Users can update QC states in the following cases:
- when a user has both Reader and QC Analyst roles
- when a user has either Folder, Project, or Site Admin roles
To assign QC states within the Biologics application:
Edit Assay Results
To edit assay results rows, access the rows of interest either by clicking the run name or the results page for the assay.
Select the rows of interest and select your option from the Manage
- Edit Selected Results in Grid: Start from a grid view of all the data for the selection; manually adjust as needed.
- Edit Selected Results in Bulk: Assign one value for a field to all the selected rows. For example, if an incorrect Day was entered for a set of runs, you could correct it in one step.
For details about using the editors for these two methods of updating results rows, see the documentation for the same feature in LabKey Sample Manager
Delete Assay Results
Specific results rows within a run can be deleted from either the grid for a specific run, or for the results page for the assay as a whole. If you want to delete an entire assay run, learn how in this topic: Biologics: Upload Assay Data
From the results grid, select the rows to delete and select Manage > Delete Selected Results
You will be reminded that deletion of rows is permanent and cannot be undone. Confirm the action in the popup to actually delete the results.