---
title: "Reference Analysis (Execution Mode)"
slug: "reference-analysis-execution-mode"
updated: 2026-09-09T13:56:59Z
published: 2026-09-09T13:56:59Z
canonical: "docs.discngine.com/reference-analysis-execution-mode"
---

> ## Documentation Index
> Fetch the complete documentation index at: https://docs.discngine.com/llms.txt
> Use this file to discover all available pages before exploring further.

# Reference Analysis (Execution Mode)

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 summary](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Setting/assay-exec-reference-analysis-home.png?sv=2026-02-06&spr=https&st=2026-11-11T00%3A35%3A39Z&se=2026-11-11T01%3A35%3A39Z&sr=c&sp=r&sig=0asXmpsmv9xcKRbbaj7wf0eMPAfdp%2Byf3YeRaM8NsRA%3D)

## From the Run Template

Before accessing the `Reference Analysis` page, some information is pre-calculated using the run template configuration:

- How the data is aggregated:
  - Aggregations define how individual data points are grouped for analysis (e.g., grouping all data points for a given sample across tested doses to calculate an IC50).
- The automatic analysis:
  - Some data may be automatically invalidated if the designer defined such rules.
- The annotation types:
  - Annotation types may be added to wells or plates, allowing you to add extra values.

## Reference Analysis

### Validate or Invalidate a Data Point

When analyzing data, you can manually invalidate data points. Select the data and click the `Invalidate` button in the top bar. The analysis will be recalculated without the invalidated data (e.g., IC50).

For more information, see the [How To: Validate or Invalidate Data guide](/public/docs/validate-or-invalidate-data).

### Add Annotation Values and Comments

You can add, edit, or delete annotation values, or add comments to a group using the left panel. See [How To: Add Annotation Values or Comments](/public/docs/add-annotation-values) for instructions.

### Update Analysis Parameters for an Aggregated Group

If needed, you can manually update the parameters used to calculate a data point for an aggregated group. See [How To: Update Analysis Parameters](/public/docs/update-analysis-parameters-for-a-group) for instructions.

## Reference Analysis Settings

Aggregations are created by the designer in the `Reference Analysis Settings` page. This page is automatically skipped in `Execution Mode`, but you can access it using the breadcrumb bar.

![Reference Analysis settings summary](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Setting/assay-exec-reference-analysis-settings.png?sv=2026-02-06&spr=https&st=2026-11-11T00%3A35%3A39Z&se=2026-11-11T01%3A35%3A39Z&sr=c&sp=r&sig=0asXmpsmv9xcKRbbaj7wf0eMPAfdp%2Byf3YeRaM8NsRA%3D)

## Next Step

              
              

You can freely navigate between `Well Validation` and `Reference Analysis` pages using the `Back to Well Validation` button. From the `Well Validation` page, continue the analysis by proceeding to the next step: [Sample Mapping step](/public/docs/sample-mapping-execution-mode).