Paired Group Test
The Paired Group Test allows the user to perform a two-sample paired t-test or Wilcoxon test, generating an Inference Report. However, this menu option is not the recommended option for a t-test; use of the General Linear Model is preferred for a more complete statistical inference test.
To run this module, type MicroArray | Inference | Other Tests | Paired Group Test.
Input Data Requirements
This function works on -Omic data types.
- Project & Data: The window includes a dropdown box to select the Project and Data object to be filtered.
- Variables: Selections can be made on which variables should be included in the filtering (options include All variables, Selected variables, Visible variables, and Customized variables (select any pre-generated Lists)).
- Observations: Selections can be made on which observations should be included in the filtering (options include All observations, Selected observations, Visible observations, and Customized observations (select any pre-generated Lists).
- Output name: The user can choose to name the output data object.
- Test type: Selecting the Test Type (available types are "TTest", "WilcoxonTest").
- Pair: The Pair column can be selected from the dropdown box (and comes from columns in the Design Table). This would be the Design Table column that is evenly paired for each group. For instance, if there were 5 subjects, and each subject had a pre-sample and post sample, a Subject column would be used as the Pair in this window.
- Treatment: The Treatment column can be selected from the dropdown box (and comes from columns in the Design Table). This would be the Design Table column that the user is interested in comparing. For instance, if there were 10 subjects, where each sample had a Pre-sample and Post-sample, the Pre/Post column would be used as the Treatment in this window.
- Control: The baseline users would like to compare other to.
- Multiplicity: The option of setting a Multiplicity test (None, FDR_BH, FDR_BY, Bonferroni, Sidak, StepDownBonferroni, StepDownSidak, and StepUp--with BDR_BH being the default option)
- Generate significant list: Checking this box generates a List of significant rows based on the test.
- Alpha level: The p value cutoff to be used for the generation of the List.
- Split the significant list by change direction: Generate 2 significant lists, split by the sign of estimates.
- Generate Fold Change:
- If FC transformation=Ratio, The foldchange values will be calculated by dividing mean case value by mean control value. the logratio will then be calculated from the foldchange.
- Otherwise, the estimates will be reported (mean case - mean control), then linear fold-change will be calculated by transforming the estimate by the specified transformation (e.g. Exp2).
The output of Paired Group Test is an Inference Report, similar to One Way Anova.