GxE Interaction

Running this process using the sf2 sample setting generates the tabbed Results window shown below. Refer to the GxE Interaction process description for more information. Output from the process is organized into tabs. Each tab contains one or more plots, data panels, data filters, and so on. that facilitate your analysis.

Tab Viewer

This pane provides you with a space to view individual tabs within the Results window. Use the tabs to access and view the output plots and associated data sets.

The following tabs are generated by this process:

•	Stability: This tab shows a plot of various stability measures for each of the genotypes.

•	G LSMeans: This tab displays estimates of LS means for the trait at each of the genotypes with confidence limits.

•	GxE LSMeans: This tab displays estimates of LS means for the trait for the Genotype x Environment interaction effect, with a line for each environment colored distinctly.

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2D Biplots: This tab displays 2-D plots of PC2 by PC1, PC3 by PC1, and PC3 by PC2, where PC1-PC3 are the first three principal components from the linear-bilinear model (AMMI, for example). In these plots and the ones on the next two tabs, genotypes are represented by blue triangles and environments are represented by red circles.

•	3D Biplot: This tab shows a 3-D plot of PC1, PC2, and PC3, the first 3 principal components from the linear-bilinear model.

•	PC1 x Mean Trait: This tab displays a biplot of PC1, the first principal component from the linear-bilinear model, by the mean of the Trait Variable.

•	Scree Plot (GxE Interaction): This tab displays the scree plot for the principal components from the linear-bilinear model, plotting the eigenvalue by principal component in red, and the cumulative proportion explained by the PCs in blue.

•	SAS Output: When there is only one Quantitative Trait selected, this tab shows the heritability calculated by PROC MIXED in SAS, and the ANOVA results from fitting the GxE model with PROC GLM.

Output Data

This process generates the following data set(s):

ANOVA Data Set: This data set contains the ANOVA statistics from fitting the GxE model.

PCA Data Set: This data set contains the principal component eigenvectors from the linear-bilinear model.

ANOVA for Linear-Bilinear Model Data Set: This data set contains the ANOVA from fitting the linear-bilinear model that includes principal components to represent the GxE component.

Predicted Values for the AMMI Models from the GxE Interaction: This data set is created when the "Output predicted values for the AMMI models option is checked. This data set contains predicted values for all the AMMI models (AMMI0, AMMI1, AMMI2, ...). These predicted values can then be used for QTL mapping as proposed by Gauch et al (2011)¹.

For detailed information about the files and data sets used or created by JMP Life Sciences software, see Files and Data Sets.

General

•	Click View Data to reveal the underlying data table associated with the current tab.

•	Click Reopen Dialog to reopen the completed process dialog used to generate this output.

•	Click Create Report to generate a pdf- or rtf-formatted report containing the plots and charts of selected tabs.

•	Click Close All to close all graphics windows and underlying data sets associated with the output.

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1

Gauch, H.G., Rodrigues, P.C. , Munkvold, J.D. , ner Heff, E.L., and Sorrells, M. (2011). Two New strategies for Detecting and Understanding QTL × Environment Interactions. Crop Science 51:96-113.