Add Sample Descriptions (Sample Sets)

You can associate sample descriptions (sample sets) with flow data and assign additional meanings to keywords.

Additional information about groups of FCS files can be uploaded in spreadsheet and associated with the FCS files using keywords.

  • To upload the data, go to the flow dashboard and click Upload Sample Descriptions.
  • If you have an existing sample set definition in a XAR format, click the upload the XAR file directly link to do so.
  • If you have a spreadsheet or other TSV (tab separated values) format file, choose the Upload Type:
    • Cut/Paste: Paste the sample information into the text box.
    • File: Browse to the file to upload.
  • The first row should contain column names, and subsequent rows should contain the data. If there is a "Name" column, it will be used as each sample's unique identifier. In the sample data download available here: Step 1: Set Up a Flow Folder, you can find the sample file "labkey-flow-demo-123/labkey-demo/Workspaces/sample-set.tsv".
  • Name Format: Choose whether to provide an expression or select ID columns to create sample names, if not provided explicitly in your TSV.
    • Expression: Provide an expression, using substitution syntax. For example:
      ${DataInputs:first;defaultValue('S')}-${now:date}-${batchRandomId}
    • ID Columns: After pasting sample set data, you will be able to choose columns from which the sample name will be constructed.
  • In the case shown below, the "AssayId" and "SampOrd" columns are the uniquely identifying columns for each sample.
  • Select a Parent Column if needed.
  • Click Submit.

Once you've uploaded the sample information, you need to associate the sample columns with the FCS file's keywords using the sample join fields.

  • Click My Flow Tutorial (or other name of your folder) to return to the flow dashboard.
  • Click Define sample description join fields and specify the join as:
Sample PropertyFCS Property
"AssayId""EXPERIMENT NAME"
"SampOrd""Sample Order"

  • Click Update.

You will now see a new column in the FCSFile table and can add it to your view:

  • Click My Flow Tutorial (or other name of your folder).
  • Click FCS Files in the Flow Summary on the right.
  • Click the Name FACSData.
  • Then select (Grid Views) > Customize Grid.
  • You should now see the columns from the Sample table that you may add to your grid.

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