LabKey SQL provides the "Statistic" method on FCS tables to allow calculation of certain statistics for FCS data.

Example: StatisticDemo Query

For this example, we create a query called "StatisticDemo" based on the FCSAnalyses dataset. (You can see a complete version of this query here: StatisticDemo.)

Create a New Query

  • Select (Admin) > Developer Links > Schema Browser.
  • Click flow to open the flow schema.
  • Click Create New Query.
  • Call your new query "StatisticDemo"
  • Select FCSAnalyses as the base for your new query.
  • Click Create and Edit Source.

Add Statistics to the Generated SQL

The default SQL simply selects all the colums:

SELECT FCSAnalyses.Name,
FCSAnalyses.Flag,
FCSAnalyses.Run,
FCSAnalyses.CompensationMatrix
FROM FCSAnalyses

  • Add a line to calculate the 'Count' statistic like this; remember to add the comma to the prior line.
SELECT FCSAnalyses.Name,
FCSAnalyses.Flag,
FCSAnalyses.Run,
FCSAnalyses.CompensationMatrix,
FCSAnalyses.Statistic."Count"
FROM FCSAnalyses
  • Click Save.
  • Click the Data tab. The "Count" statistic has been calculated using the Statistic method on the FCSAnalyses table, and is shown on the right.

You can flip back and forth between the source, data, and xml metadata for this query using the tabs in the query editor.

Run the Query

From the "Source" tab, to see the generated query, either view the "Data" tab, or click the Execute Query button. To leave the query editor, click Save & Finish.

The resulting table includes the "Count" column on the right:

View this query applied to a more complex dataset. The dataset used in the Flow Demo has been slimmed down for ease of use. A larger, more complex dataset produces a more interesting "Count" column, as seen in this table and the screenshot below:

Example: SubsetDemo Query

It is possible to calculate a suite of statistics for every well in an FCS file using an INNER JOIN technique in conjunction with the "Statistic" method. This technique can be complex, so we present an example to provide an introduction to what is possible.

Create a Query

For this example, we use the FCSAnalyses table in the Peptide Validation Demo, a more complex demo than the one used in the Flow Tutorial. We create a query called "SubsetDemo" using the "FCSAnalyses" table in the "flow" schema and edit it in the SQL Source Editor.

SELECT 
FCSAnalyses.FCSFile.Run AS ASSAYID,
FCSAnalyses.FCSFile.Sample AS Sample,
FCSAnalyses.FCSFile.Sample.Property.PTID,
FCSAnalyses.FCSFile.Keyword."WELL ID" AS WELL_ID,
FCSAnalyses.Statistic."Count" AS COLLECTCT,
FCSAnalyses.Statistic."S:Count" AS SINGLETCT,
FCSAnalyses.Statistic."S/Lv:Count" AS LIVECT,
FCSAnalyses.Statistic."S/Lv/L:Count" AS LYMPHCT,
FCSAnalyses.Statistic."S/Lv/L/3+:Count" AS CD3CT,
Subsets.TCELLSUB,
FCSAnalyses.Statistic(Subsets.STAT_TCELLSUB) AS NSUB,
FCSAnalyses.FCSFile.Keyword.Stim AS ANTIGEN,
Subsets.CYTOKINE,
FCSAnalyses.Statistic(Subsets.STAT_CYTNUM) AS CYTNUM,
FROM FCSAnalyses
INNER JOIN lists.ICS3Cytokine AS Subsets ON Subsets.PFD IS NOT NULL
WHERE FCSAnalyses.FCSFile.Keyword."Sample Order" NOT IN ('PBS','Comp')

Examine the Query

This SQL code leverages the FCSAnalyses table and a list of desired statistics to calculate those statistics for every well.

The "Subsets" table in this query comes from a user-created list called "ICS3Cytokine" in the Flow Demo. It contains the group of statistics we wish to calculate for every well.

View Results

Results are available in this table.

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