ANOVA method is applying a specified log normal model to all the features.

ANOVA

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ANOVA dialog

To setup ANOVA model, select factors from sample attribute. The factors can be categorical or numeric attribute. Click on a check button to select and click Add factors button to add it to the model (Figure 14).

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Low-expression feature and Multiple test correction sections are the same as the matching GSA advanced option, see above GSA advanced options.

Report option

• • User only reliable estimation results: There are situations when a model estimation procedure does not fail outright, but still encounters some difficulties. In this case,  it can even generate p-value and fold change on the comparisons, but they are not reliable, i.e. they can be misleading. Therefore, the default of Use only reliable estimation results is set Yes.

  • Display p-value for effects: If set to No, only the p-value of comparison will be displayed on the report, the p-value of the factors and interaction terms are not shown in the report table. When you choose Yes in addition to the comparison’s p-value, type III p-values are displayed for all the non-random terms in the model.

  • Report partial correlations: If the model has a numeric factor(s), when choosing Yes, partial correlation coefficient(s) of the numeric factor(s) will be displayed in the  result table. When choosing No,  partial correlation coefficients are not shown.

  • Data has been log transformed with base: showing the current scale of the input data on this task.

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Since there is only one model for all features, so there is no pie charts design models and response distribution information. The Gene list table format is the same as the GSA report.