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Select menu: Stats | Meta Analysis | AMMI

Watch our video on creating AMMI biplots.

For data classified by two factors, AMMI is used to fit a model which involves the Additive Main effects of ANOVA along with the Multiplicative Interaction effects of principal components analysis (PCA). The method is used when analysing data from a series of trials with crop genotypes. A principal components model is fitted to the residuals from the ANOVA and the resulting scores, called the I (for interaction) PCA scores, are calculated for both the genotypes and the trials or environments.

  1. After you have imported your data, from the menu select 
    Stats | Meta Analysis | AMMI.
    After you have imported your QTL data, select
    Stats | QTLs (linkage/Association) | Data Exploration | Phenotypic Data | AMMI
  2. Fill in the fields as required then click Run.

You can set additional Options then after running, you can save the results by clicking Save.

The dialog can handle replicate observations that make up the genotype x environment means by specifying the replicate observations, and a replicate factor using the Replication box. When constructing the analysis-of-variance table, AMMI assumes that the replicates arise from the use of a randomized block design within each environment. No missing values are allowed, and there must be equal replication.

Available data

This lists data structures appropriate to the current input field. It lists either factors for use in specifying the genotypes, environments and replication, or variates for specifying the data. The contents will change as you move from one field to the next. Double-click a name to copy it to the current input field or type the name.


Specify a variate containing the data.


A factor to specify the genotypes.


A factor to specify the environments.


Specify a factor for the replication; this should be left blank if the data comprises of just the genotype by environment means.

Action Icons

Pin Controls whether to keep the dialog open when you click Run. When the pin is down  the dialog will remain open, otherwise when the pin is up  the dialog will close.
Restore Restore names into edit fields and default settings.
Clear Clear all fields and list boxes.
Help Open the Help topic for this dialog.

See also

Updated on June 12, 2019

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