Permutation TTest Algorithm

Performed on a set of non-negative numbers and labels of size N. There must be two specific labels. Label 1 must be 1 and label 2 must be 2. There can also be any other labels that will be ignored.

Permutation T value

1. Find the number and sum of each group.
   • Na: number of values in group 1
   • Nb: number of values in group 2
   • Sa:
   • Sb:
   • SSa:
   • SSb:
2. Compute the sample mean of each group.
   • Ma:
   • Mb:
3. Compute the variance for each group.
4. Estimate the variance
   • varA:
   • varB:
   • Var:
5. Estimate the standard deviation (stDev):
6. t:

Permutation T probability

1. Calculate raw P value based on original grouping of each gene.
   =
2. Randomly regrouping each gene.
   The size in each group stays the same as the original, each sample can only appare once in each group, number of regrouping depends on user.
3. For each regrouped gene, recalculate P value.
   =
4. Count if less than or equals to .
   count = number of <=
5. Calculate permutation P value.
   PP-value =
6. Rank PP-value by ascending order, calculate False Discovery Rate P value.
   FDR P-value = *PP-value

summary of running time

sample size	group size	permutation time	running time
10	5 vs. 5	252	0.01
10	5 vs. 5	5,000	0.406
20	10 vs. 10	10,000	0.56
20	10 vs. 10	1,847,560	87.746
50	25 vs. 25	10,000	1.261
50	25 vs. 25	50,000	14.703

-- JoanZhang - 16 Aug 2004