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.