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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:

- P-value:

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

N = totalGene

= - Randomly regrouping each gene.

The size in each group stays the same as the original, each sample only appears once in each group, number of regrouping depends on user. - For each regrouped gene, recalculate P value.

= - Count if less than or equals to for each gene.

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

PP-value = - Rank PP-value by ascending order, calculate unadjusted T probability of each gene from the gene with largest rank to smallest rank.

P-value = *PP-value

if >=1, then set = 1

if > , then =

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

N = totalGene

: - Randomly regrouping each gene.

The size in each group stays the same as the original, each sample only appears once in each group, number of regrouping depends on user. - For each regrouped gene, recalculate T value.

: - for each , calculate number of T values of all permuted genes >=

count = permuted T value of all genes >= - Estimate P-value of

estP-value = - Rank estP-value by ascending order, calculate adjusted T probability of each gene from the gene with largest rank to smallest rank.

P-value = *estP-value

if >=1, then set = 1

if > , then =

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 |

Topic revision: r4 - 09 Nov 2004, JoanZhang

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