To work with assay data in LabKey, it is helpful to review some of the terminology used to describe the various grouping levels for assay data:
- Assay Results: The individual data elements from an instrument, for example the intensity of a spot or well. Assay instruments typically output a lot of results each time a sample is run.
- Assay Runs: Data imported representing a single instrument run, typically but not necessarily contained in a single file. An operator may be required to enter properties at the time of import, depending on the instrument type.
- Assay Batches: A set of runs uploaded in a single session; some properties may be common to the entire batch. A single run can still be considered a batch and still uses batch properties when uploaded by itself.
Once you have uploaded assay data, you will be taken first to the Runs grid, which is the "middle" level grouping, between Results (the most detailed grid view) and Batches (the most general view).
The Runs grid provides a number of links to manage and explore the assay data:
- Clicking a link in the Assay Id column, such as "Run4", takes you to the Results grid for that run.
- Clicking the Flag icon toggles the flag indicating there is a need to review the run for possible problems. When you flag a row, you may enter a comment. A flagged row shows a colored icon; hover to see the comment entered. To delete a flag, click it, delete the comment and click OK.
- Clicking the Flow Chart icon (in the unnamed column between Flag and Assay Id) takes you to details about the run, including a graphical representation of the run. For example, clicking the graph link for Run1 shows the following. Notice that the graph assumes that each unique date in the assay data represents a different specimen.
- Return to the assay runs grid using the back button in your browser, or by clicking the folder link Assay Tutorial, then GenericAssay in the assay list.
The Results grid shows actual assay data originally encoded in the Excel files, now captured by the assay design.
- From the Runs grid, in the Assay Id column, click Run3.
- You are taken to the assay Results grid. Only results for the selected run are shown.
- Notice that a filter "lozenge" is shown above the grid, reading " Run = ##" The system generated RowID number is shown instead of the name. In the screencap below it reads "Run = 9".
- To see all results across all runs, clear the filter by clicking the icon.
- Use the Results grid to create reports and visualizations.
- To see a quick best guess visualization for this tutorial data, click one of the column headers M1, M2, or M3 and select Quick Chart. For the column M2 results for all runs, LabKey Server's best guess is a box and whisker plot that will look something like this:
- Explore the customizations available using the Chart Type and Chart Layout links in the chart designer.
- To return to the Results grid, click the Back button on your browser (or use Assay Tutorial to return to the main folder page, click GenericAssay in the Assay List, then View Results).
- There is much more you can do with the Results grid of assay data -- explore the buttons and menus above the grid, such as (Grid Views), Reports and Charts, and Export.
- Return to the main page by clicking Assay Tutorial, click GenericAssay, then View Batches to see a grid view of all batches imported.
- In this tutorial, we imported only a single batch of four runs.
- In practice, there might be daily batch uploads, multiple batches from different instrument operators, or different batches of runs from different instruments.
- The batch grid can be customized, but by default shows the run count as well as batch properties specified on import.
- Click the batch Name to return to the runs grid, filtered to only show runs from that batch. (Note that if runs were deleted and imported as part of a later batch, the earlier batch will no longer show those runs.)