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- 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:

- Compute the sample mean of each group.
- Ma:
- Mb:

- Compute the variance for each group.
- Estimate the variance
- varA:
- varB:
- Var:

- Estimate the standard deviation (stDev):
- t:

- Calculate raw P value based on original grouping of each gene.

= - 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. - For each regrouped gene, recalculate P value.

= - Count if less than or equals to .

count = number of <= - Calculate permutation P value.

PP-value = - 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

if P-value of rank n > P-value of rank n+1, then p-value of rank n = P-value of rank n+1

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 |

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Topic revision: r5 - 28 Oct 2004, JoanZhang

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