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This topic describes how to work with assay data runs and results within the Sample Manager application.
First open the assay design of interest, by using the main menu or assay dashboard then then clicking the assay design name. Click the Runs
tab in the upper left to manage runs.
Click the name of an individual run to manage it. From this run details page, users with "Editor" or "Admin" access can reimport a run, and see and manage results for that run.
Edit Run Properties
If your assay has editable runs
and you have sufficient permissions, you can edit run details.
To edit run properties for a single run, click the name of the run, then use the (Edit)
icon in the Run Details
panel to open them for editing. You will see an entry panel you can use to make changes.
Click Save Run Details
Bulk Edit Run Properties
Provided your assay has editable runs
and you have sufficient permissions, you can also edit run properties in bulk.
- Make sure you're on the Runs tab.
- Select one or more runs, then choose either:
Learn about these interfaces in the section below about editing Result data
If you have a change of data or metadata after importing a run, and have editable runs and/or results, you may be able to make the change directly. However, if your runs/results are not editable, you can import a revised version of the run as follows. LabKey Sample Manager will track run re-imports and maintain data integrity.
Opening the run details (shown above) and select Manage > Re-Import Run
You will see the interface from when you originally imported the run
, including the values and datafile previously entered. Make changes as needed and click Re-Import
A note about event logging:
When you re-import an assay run, two
new assay events are created:
- Assay Data Re-imported: This event is attached to the "old run" that is being replaced.
- Assay Data Loaded: This event is for the "new run" you import.
To delete a run, either:
- Start from the run details page and use Manage > Delete Run
- Start from the Runs or Overview tab, select one or more runs and choose Edit > Delete.
- In the popup, you can enter Reason(s) for deleting which will be included in the audit log.
- Confirm the deletion by clicking Yes, Delete.
Note that a run cannot be deleted if it is referenced in an Electronic Lab Notebook
. You will see a message indicating why the option is unavailable.
The result data for your assay is available on the Results
tab. Results are individual rows within runs. You cannot add results rows within the user interface. To do so, either import a new run containing the results, or add them to an existing run by reimporting the run
after adding the additional rows to the run data file.
Edit Selected Results in Grid
If your assay has editable results
, and you have sufficient permissions, you can select one or more rows using checkboxes and select Edit > Edit in Grid
A grid will be shown, with a row for each row you selected, allowing you to edit the necessary values. Click Finish Updating # Results
to save your changes.
Learn more about using editable grids in this topic:
Edit Selected Results in Bulk
If you are editing a number of rows to insert shared values, select the desired rows with checkboxes and select Edit > Edit in Bulk
An editing popup will let you select which field or fields you want to batch update. By default, all fields are disabled; choosing Enabled
will let you enter a value to assign for that field in all rows. Shown here, the MCV field will be updated with a shared value, but all other fields left unchanged.
After entering updated values, you can leave the bulk popup using either:
- Edit with Grid to switch to updating in a grid format (with the bulk changes you just made already applied). Use this option if you want to make individual as well as bulk row changes.
- Be sure to click Finish Updating # Results when finished with the grid update to save both the bulk changes AND individual changes you made.
- Update Results if no further editing is needed. The bulk updates will be saved.
To delete one or more rows of results within any run, either open the run from the Runs tab or find the desired rows on the Results tab. Use sorting and filtering
to help you isolate rows of interest.
Check the box(es) for the row(s) you want to delete and select Edit > Delete
. In the popup, you can enter Reason(s) for deleting
which will be included in the audit log. Confirm the deletion by clicking Yes, Delete
Note that you can only delete 10,000 assay results in one operation. To delete more than that, perform the deletion in batches.
Work with Samples from Assay Results
From the page of assay results, you can select a desired set of rows and then use the Samples
menu to work with the set of samples mapped to those results.
View Assay Data for a Sample
On the details page for any Sample, click the Assays
tab to see data about that specific sample. There is an Assay Run Summary
tab showing the number of runs per assay type. In addition, a tab for each assay type lets you browse the collected profile of results.
From any assay-specific tab, you can also Import Data
for any assay that can be linked to samples of this type, regardless of whether there are runs of that type yet.
View Assay Results for Selected Samples
From a grid of samples, including tabbed grids showing multiple sample types like picklists, you can select desired samples, then choose Reports > View Assay Results for Selected
The report includes an Assay Run Summary
tab, showing the count of runs of each assay type for each sample. This can provide a handy dashboard for confirming that data analysis is on track for a mixed set of samples.
On assay-specific tabs, you can see all the assay results for your selected group of samples.
Exporting any tab from this report to Excel offers the option to include any or all of the tabs. Multiple tabs will be exported as a multi-sheet Excel file