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There are situations when a model estimation procedure does not outright fail, but still encounters some difficulties. In this case, it can even generate p-value and fold change for the comparisons, but those values are not reliable, and can be misleading. It is recommended to use only reliable estimation results, so the default option for Use only reliable estimation results is set Yes.

Model types configuration

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Low-expression feature and Multiple test correction sections are the same as the 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, even it can generate p-value and fold change on the comparisons, but they are not reliable, they can be misleading. It is recommended that only reliable estimation results should be used, so the default of Use only reliable estimation results is set Yes
• Display p-value for effects: When you choose No, only p-value of comparison will be displayed on the report. 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.

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