Premium Feature — Available with all Premium Editions of LabKey Server. Learn more or contact LabKey.

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 link 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 Type

This method extends the information about the flow samples to include participant ids, visits, etc. It uses a sample type as a mapping table, associating participant/visit metadata with the flow vials.

For example, if you had Flow data like the following:

TubeNamePLATE_IDFlowJoFileIDand so on...

You could extend the fields with a sample type like

  • Add a sample type that contains the ptid/visit data.
  • Associate the sample type with the flow data (FCS files).
    • Under Assign additional meanings to keywords, click Define/Modify Sample Description Join Fields.
    • On the left select the vial name in the flow data; on the right select vial name in the sample type. This extends the descriptions of the flow vials to include the fields in the sample type.
    • For an example see: Associate the Sample Type 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 link to a study. Click the run you wish to link. You may need to use (Grid Views) > Customize Grid to add the ptid/visit fields.
  • To link to study: select from the grid and click Link to Study.

4. Add Participant/Visit Data During the Link-to-Study Process

You can manually add participant/visit data as part of the link-to-study wizard. For details see Link Assay Data into a Study.

Related Topics

Was this content helpful?

Log in or register an account to provide feedback

expand allcollapse all