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.