Biologics: Work with Assay Data: /Documentation/Archive/22.3

Biologics: Work with Assay Data

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
Assay Quality Control
Edit Assay Results
Delete Assay Results

Assay Data Dashboards

Click Assays 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.

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Any archived, or inactive, assay designs are only included when you click the All tab.

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:

Navigate to the assay run view page. (Cell Viability runs are shown below.)
Select one or more runs.
Select Manage > Update QC States. (Admins will see Manage > Update QC States, while QC Analysts will see only the Update QC States button.)

In the popup dialog, use the dropdown menu to select the QC state. This state will be applied to all of the runs selected.
Optionally add a comment.
Click Save changes.

The QC states will be reflected in the runs data grid. Admins and QC Analysts will see all of the runs, as shown below.

It should be noted that if some of the QC states are not marked as "Public Data", they will not be included in the grid when viewed by non-admin users. For example, if "Not Reviewed" were marked as not public, the reader would see only the runs in public states:

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 menu:

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.

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