Hi Fran,

For the NBS, 10,000 permutations is more than sufficient. Even 5,000 should be enough.

However, when using FDR, very substantially more permutations should be generated, otherwise the results will not be reliable. For this reason, we will use a parameteric version of FDR is future versions of the software.

Sample size should not be a major factor determining the number of permutations; unless your sample size is very small, in which case all possible permutations can be enumerated.

Andrew


Originally posted by francesca sibilia: