TTEST: T-test

Parameter Information


Group Assignments

Group Selection Controls

This set of buttons permits each experiment to be placed into group A, group B, or neither group. If an experiment is placed in neither group it will be ignored for the purposes the analysis.

Note that groups A and B must each have at least two members following the assignment.

Save Grouping

The save grouping button allows you to save the grouping to file. This is particularly useful when there are many experiments.

Load Grouping

This button allows you to select and load a saved grouping.

Reset

The reset button returns all of the group selection control buttons to Group A, the initial state.

Degree of freedom calculation

This option applies to between subjects t-test only. By default, degree of freedom is calculated on a gene by gene basis assuming that the two groups have unequal variances. The other option assumes equal variances of the two groups, and calculates degree of freedom as (nA + nB - 2), where nA and nB are the number of valid values in groups A and B respectively.

P-Value Parameters

This set of controls are used to indicate the method by which p-values are determined for each gene and allows the input of the critical p-value.

p-values can be computed either from the theoretical t-distribution, or from permutations of the data for each gene between the two groups.

p-values based on t-distribution

Using this option a gene's p-value is taken directly from the theoretical t-distribution based on the gene's calculated t-value.

p-values based on permutation

Using this option a gene's p-value is determined by forming a distribution based on permutations of the data for that gene. The permutations allow each value in the expression vector in group A or group B to be randomly placed into either group (the size of each group is conserved). t-values are constructed following each permutation to construct a distribution which is used to generate p values for each gene based on it's t-value.

If permutations are used, two buttons allow you to select to permute the values a number of times indicated or to permute the values a number of times equal to the maximum number of permutations possible.

Critical p-value

This text field allows you to enter the alpha or critical p-value.

P-Value Corrections

The p-values for each p can be adjusted to correct for the large number of observations (genes) and the increased possibility of considering a gene without a real significant change to be considered significant. Three options are given for this correction.

Just Alpha (no correction)

Using this option the alpha is not altered.

Standard Bonferroni Correction

In the standard Bonferroni correction, the user-specified alpha is divided by the number of genes to give the critical p-value. This is much more stringent than using an uncorrected alpha.

Adjusted Bonferroni Correction

In the adjusted Bonferroni correction, the t-values for all the genes are ranked in descending order. For the gene with the highest t-value, the critical p-value becomes (alpha / n), where n is the total number of genes; for the gene with the second-highest t-value, the critical p-value will be (alpha/ n-1), and so on. The stringency of this correction falls somewhere between no correction and the Standard Bonferroni.

Hierarchical Clustering

This check box selects whether to perform hierarchical clustering on the elements in each cluster created.