Configure the settings of the Analysis tab of the Extensible Normalization app to apply a normalization method

Prior to this task:

✔ Extensible Normalization app must be opened.

1️⃣ Extensible Normalization – Analysis tab ➡ Data Configuration ➡ select Control column Feature columns Result column name ➡ type new name
2️⃣ Extensible Normalization – Analysis tab ➡ Data Configuration ➡ select  [Next]
3️⃣ Extensible Normalization – Analysis tab ➡ Normalization Settings ➡ select Intra plate method Inter plate method Negative controls Positive controls
4️⃣ Extensible Normalization – Analysis tab ➡ select  [Apply]

Supporting Knowledge

Note: The Extensible Normalization app does not apply different methods when there are multiple types of values; the normalization selected will be applied to all variables.

Note: The Extensible Normalization app will auto-execute in a Workflow if all parameters are configured beforehand.

Optionally, the user can exclude controls from the Intra plate method of normalization. From the Extensible Normalization – Analysis tab, under Intra plate method, select the [Excluded controls] toggle.

Optionally, the user can access shared methods that allow them to load custom-defined normalization expressions created via the Calculations Explorer and shared in the Metastore. From the Extensible Normalization – Analysis tab, under Inter plate method, select the [Show shared methods] toggle.

Note: More than one type of negative and/or positive controls can be selected.

Optionally, from the Extensible Normalization – Analysis tab, under the Normalization Settings area, the user can mark data to select wells of interest and mark points in the analysis for exclusion or inclusion by selecting the [Exclusion] button and the [Inclusion] button, respectively. To reset the points excluded or included, select the  [Reset] button.

Optionally, from the Visualization tab, the user can use the available toggles for further modifications. From the Extensible Normalization – Analysis tab, select  [Visualization]. From the Extensible Normalization – Visualization tab, under Toggle visualization groups, select the ["visualization name"] toggles to turn the display of the visualizations on and off.

Additionally, from the Extensible Normalization – Visualization tab, under Visualization settings, select the [Selected Feature label] toggle to display the feature's value as a label in the Plate view scatter plot. 

Additionally, from the Extensible Normalization – Visualization tab, under the Show Filter panel, the user can turn on the Filters panel by selecting the [Filter Panel] toggle. This option enables the user to filter out data to perform further exploration. Selected filters will be applied to the Plate layout visualizations. Select the  [reset filters] button to reset all the active filtering.

When multiple features are selected on the Feature columns dropdown, under the Data Configuration, the Result column name text box will go away, and the default prefix will be set to "Normalized." However, the user can change the prefix. To do so, from the Extensible Normalization – Analysis tab, select [Configuration]. From the Extensible Normalization – Configuration tab, under Result column prefix, type a new name.