NonpaR: Nonparametric Tests
Significance Parameters
Alpha Value
The alpha value is a p-value cutoff. p-values below this value are considered as
justification for rejection of the test's null hypothesis. Lowering the alpha value, or critical p-value, makes the test
more stringent by limiting chance of a single type two error.
FDR: False Discovery Rate (when available)
The False Discovery Rate (FDR) reports an estimate of the fraction of false positives among a set of genes called signficant.
This option uses the Benjamini-Hochberg correction which is described as a correction on the p-value such that the FDR for
the collection of genes with p-values less than a particular gene i, is less than the corrected p-value for gene i. The FDR
estimates the number of false positives such that if you call 100 genes positive and the FDR is 0.05 then it is estimated
that 5 genes or fewer are falsely called significant.
There are two options for FDR, one in which you supply and FDR prior to the analysis, and a second option that supports
a user interface to permit balancing the number of significant calls with FDR following computation of the results. This second
option presents a graph of FDR vs. number of significant genes.