# 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
if P-value >=1, then set P-value = 1

#### 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
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Topic revision: r4 - 27 Oct 2004, JoanZhang

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