For Flow data to be added to a study, it must include participant/timepoint ids or specimen ids, which LabKey Server uses to align the data into a structured, longitudinal study. The topic below describes four available mechanisms for supplying these ids to Flow data.
1. Add Keywords Before Import to LabKey
Add keywords to the flow data before importing them into LabKey. If your flow data already has keywords for either the SpecimenId or for ParticipantId and Timepoints, then you can copy the Flow data into a study without further modification.
You can add keywords to an FCS file in most acquisition software, such as FlowJo. You can also add keywords in the WSP file, which LabKey will pick up. Use this method when you have control over the Flow source files, and if it is convenient to change them before import.
2. Add Keywords After Import to LabKey
If your flow data does not already contain the appropriate keywords, you can add them after import to LabKey Server. Note this method does
not change the original FCS or WSP files. The additional keyword data only resides inside LabKey Server. Use this method when you cannot change the source Flow files, or when it is undesirable to do so.
- Navigate to the imported FCS files.
- Select one or more files from the grid. The group of files you select should apply to one participant.
- Click Edit Keywords.
- Scroll down to the bottom of the page and click Create a New Keyword.
- Add keywords appropriate for your target study. There are three options:
- Add a SpecimenId field (if you have a Specimen Repository in your study).
- Add a ParticipantId field and a Visit field (if you have a visit-based study without a Specimen Repository).
- Add a ParticipantId field and a Data field (if you have a based-based study without a Specimen Repository).
- Add values.
- Repeat for each participant in your study.
- Now your FCS files are linked to participants, and are ready for addition to a study.
For details see
Edit Keywords.
3. Associate Metadata Using a Sample Set
This method extends the information about the flow samples to include participant ids, visits, etc. It uses a sample set as a mapping table, associating participant/visit metadata with the flow vials.
For example, if you had Flow data like the following:
| TubeName | PLATE_ID | FlowJoFileID | and so on... |
|---|
| B1 | 123 | 4110886493 | ... |
| B2 | 345 | 3946880114 | ... |
| B3 | 789 | 8693541319 | ... |
You could extend the fields with a sample set like
| TubeName | PTID | Date | Visit |
|---|
| B1 | 202 | 2009-01-18 | 3 |
| B2 | 202 | 2008-11-23 | 2 |
| B3 | 202 | 2008-10-04 | 1 |
- Add a sample set that contains the ptid/visit data.
- Associate the sample set with the flow data (FCS files).
- Under 5. Assign additional meanings to keywords, click Define Sample Description Join Fields.
- On the left select the vial name in the flow data; on the right select vial name in the sample set. This extends the descriptions of the flow vials to include the fields in the sample set.
- For an example see: Associate the Sample Set Descriptions with the FCS Files.
- Map to the Study Fields.
- Under Manage, click Edit Metadata.
- For an example, Set Metadata.
- To view the extended descriptions: Under Analysis Folders, click the analysis you want to copy to a study. Click the run you wish to copy. You may need to use (Grid Views) > Customize Grid to add the ptid/visit fields.
- To copy to study: select from the grid and click Copy to Study.
4. Add Participant/Visit Data During the Copy-to-Study Process
You can manually add participant/visit data as part of the copy-to-study wizard. For details see
Copy Assay Data into a Study.
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