--- title: "Reference Analysis (Design Modes)" slug: "reference-analysis-design-modes" updated: 2026-09-09T13:55:32Z published: 2026-09-09T13:55:32Z canonical: "docs.discngine.com/reference-analysis-design-modes" --- > ## 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 (Design Modes) 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](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Setting/assay-design-ref-ana-settings-aggregate-1.png?sv=2026-02-06&spr=https&st=2026-11-10T22%3A02%3A25Z&se=2026-11-10T23%3A02%3A25Z&sr=c&sp=r&sig=gmQhgP942UiuwG2uhalM7mScghEUDskvMH5nz%2F8hBIo%3D) - Click `Add Aggregation` to add it to the list ![Settings aggregate 2](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Setting/assay-design-ref-ana-settings-aggregate-2.png?sv=2026-02-06&spr=https&st=2026-11-10T22%3A02%3A25Z&se=2026-11-10T23%3A02%3A25Z&sr=c&sp=r&sig=gmQhgP942UiuwG2uhalM7mScghEUDskvMH5nz%2F8hBIo%3D) 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](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Setting/assay-design-ref-ana-settings-add-analysis.png?sv=2026-02-06&spr=https&st=2026-11-10T22%3A02%3A25Z&se=2026-11-10T23%3A02%3A25Z&sr=c&sp=r&sig=gmQhgP942UiuwG2uhalM7mScghEUDskvMH5nz%2F8hBIo%3D) 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](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Setting/assay-design-ref-ana-settings-summary.png?sv=2026-02-06&spr=https&st=2026-11-10T22%3A02%3A25Z&se=2026-11-10T23%3A02%3A25Z&sr=c&sp=r&sig=gmQhgP942UiuwG2uhalM7mScghEUDskvMH5nz%2F8hBIo%3D) - 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](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Setting/assay-design-ref-ana-home.png?sv=2026-02-06&spr=https&st=2026-11-10T22%3A02%3A25Z&se=2026-11-10T23%3A02%3A25Z&sr=c&sp=r&sig=gmQhgP942UiuwG2uhalM7mScghEUDskvMH5nz%2F8hBIo%3D) On this page, you can: - Add automatic analysis to your run (e.g., automatic invalidations). See [Automatic Analysis in Well Validation](/public/docs/well-validation-design-modes#automatic-analysis). - Add an annotation to your run (to manually add information). See [Annotations in Well Validation](/public/docs/well-validation-design-modes#annotations). - Edit experimental conditions if needed ([Experimental Conditions documentation](/public/docs/experimental-conditions-overview-design-modes)). ### Create Visualization Templates As a designer, you can create and update Spotfire Templates for use in design and execution modes. - See [Administration documentation](/public/docs/create-or-update-a-spotfire-template) for creating/updating Spotfire templates. You can also switch templates and use fullscreen mode ([How To documentation](/public/docs/visualize-my-data-and-change-template)). ### 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](/public/docs/update-analysis-parameters-for-a-group). ### 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](/public/docs/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](/public/docs/add-annotation-values). ## 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 design of the run by going to the next step: [Sample Mapping](/public/docs/sample-mapping-design-modes).