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Reference Analysis

The reference analysis step is used to analyze the reference wells of your plates, check their quality, invalidate, and annotate them. This step is available only if at least one reference well is defined in the plate mapping step.

Reference Analysis Settings

On the settings page, you define one or more aggregations and link analyses (calculations) to analyze your references.

Aggregations determine how data points are grouped for analysis. For example:

  • Grouping all data points for a sample across tested doses to calculate an IC50
  • Combining all replicates of the same measurement to compute statistics

Create an Aggregation

To create an aggregation:

  • Choose a name (default: Aggregation#1)
  • Select parameters for the aggregation (e.g., plate index, plate name, experimental condition)

Settings aggregate 1

  • Click Add Aggregation to add it to the list

Settings aggregate 2

You can add more aggregations by clicking New Aggregation in the summary region. Aggregations are displayed in the summary region on the left.

Add an Analysis

In the analysis region, add a calculation to a specific aggregation:

  • Select your aggregation from the list
  • Choose one or more series to analyze
  • Select the analysis to perform (e.g., Dose response, statistics)
  • Enter the analysis parameters (e.g., dose response parameters)
  • Click Add Analysis to add it to the list

Settings add analysis

You can add more analyses using the same method. Analyses are displayed in the summary region on the left.

Summary

In the summary region, view the list of aggregations and analyses you have created.

Settings summary

  • Use the Aggregation Selection tab to display all aggregations or only the selected one
  • For a selected aggregation, you can:
    • Delete the aggregation
    • Delete an analysis from the aggregation
    • Update analysis parameters

Validate the step by clicking the Reference Analysis button.

Reference Analysis

Add Calculation and Data

After calculations are complete, you are redirected to the reference analysis page.

Reference analysis

On this page, you can:

Create Visualization Templates

As a designer, you can create and update Spotfire Templates for use in design and execution modes.

You can also switch templates and use fullscreen mode (How To documentation).

Update Analysis for an Aggregated Group

You can manually update parameters used to calculate data for one or more aggregated groups. See How To Update Analysis Parameters.

Validate or Invalidate a Data Point

To manually invalidate data, select the data and click the Invalidate button in the top bar. The analysis will be recalculated (e.g., IC50). See How to Validate or Invalidate Data.

Add Annotation Values and Comments

You can add, edit, or delete annotation values or comments using the left panel. See How To Add Annotation Values or Comments.

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