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When the data are read as 3-way parallel, 4-way parallel, or Anyway parallel, and when the Main-effect ANOVA option under the main menu of "Anyway" is selected, the following form will appear:
This interface allows the researcher to choose any of the traits and to conduct ANOVA with regard this trait for any factors that are selected from the list of factors in the data. In this example, location and genotype are selected as factors. GGEbiplot will treat the genotype*location combinations as treatments and genotype and location as factor to generate and ANOVA table, and to test the significance of the treatment, genotype, and location. GGEbiplot will also conduct multiple comparisons among the treatments, the genotypes, and the environments.
GGEbiplot does the multiple comparison for any factor (e.g., genotype) by calculating an LSD-standardized mean value across other factors for each genotype such that if two genotypes differ by 1.0 or more, they will be considered as statistically different at the 0.05 or 0.01 level of significance.
The results will be written into the log file, which can be opened in Excel by clicking the "Open Log File" under the main menu bar "Help".