TwoGroupTest.pdf

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Two Group Test

Overview

The Two Group Test module allows the user to perform a two-sample t-test or Wilcoxon test to determine whether the means of two independent groups differ, and will generate an Inference table.

However, this menu option is not the recommended method 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 | Two Group Test.

TwoGroup menu.png

Input Data Requirements

This module works on -Omic data types. The Design metadata table should have a column by which the samples can be sub-grouped.

General Options

TwoGroupTest0.png

Input/Output

  • 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.


Options

  • Test Type: Sets the Test type (TTest, WilcoxonTest, KSTest and ModeratedTTest). TTest and ModeratedTTest are parametric tests, while the WilcoxonTest and KSTest are non-parametric tests.
  • Group: Choose the factor from the design table to test whether two levels in the factor have different means.
  • Compare to: Choose which covariate level to compare to.
  • Multiplicity: The option allows the user to specify the Multiplicity test (None, FDR_BH, FDR_BY, Bonferroni, Sidak, StepDownBonferroni, StepDownSidak, and StepUp--with BDR_BH being the default option)
  • Assume equal variance: Checking this box assumes samples with different factor levels share the same error variance.(checked by default).
  • Generate significant list: Checking this box generates a List of significant rows based on the test.
  • Calculate medians: Selecting this option will compare the medians of different groups, rather than the means, of different groups.
  • Alpha level: Specify the p-value cutoff to be used for the generation of the List.
  • Split the significant list by change direction: Generate two significant lists, split by the sign of estimates.
  • Generate fold change: Checking this box will generate a column of fold-change values in the output table. The fold change transformation options include Exp2, Exp. Exp10 and Ratio.
  • Bootstrap without replacement: The user can select this method for assigning measures of accuracy to sample estimates.
    • Group 1 Size - Number of samples to include in group 1
    • Group 2 Size - Number of samples to include in group 2
    • Bootstrap number (10-100000): As many samples as is reasonable given available computing power and time should be used.

Output Results

Clicking "Submit" will generate a Table in the Inference tab of the Solution Explorer for the requested test as shown below:

TwoGroupTest1.png

The user can append other Views, such as a Volcano plot:

Microarray TwoSample VolcanoPlot.png

In addition, several Views are available in the task tab, including the Intensity/Estimate View:

Microarray TwoSample Visualizations.png Microarray TwoSample IntensityVsEstimate.png


OmicScript

Two Group Test

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