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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.

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• • 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 Report 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.

  • Apply shrinkage to error term variance: When you select Yes, the analysis model is lognormal with shrinkage (the same as the GSA distribution type default option). You cannot include random effects in the model when choose Yes. If there is numeric factors in the model, the partial correlations  cannot be reported on the numeric factors when choose Yes. This options is recommended for small sample size design.

  • 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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