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: Obtain the Sample Data Files, 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:
- 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.
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 Property||FCS Property|
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.