sage.test {statmod} | R Documentation |

## Compare Two SAGE Libraries

### Description

Compute p-values for differential expression for each tag between two serial analysis of gene expression (SAGE) libraries.

### Usage

sage.test(x, y, n1=sum(x), n2=sum(y))

### Arguments

`x` |
integer vector giving counts in first library.
Non-integer values are rounded to the nearest integer. |

`y` |
integer vector giving counts in second library.
Non-integer values are rounded to the nearest integer. |

`n1` |
total number of tags in first library.
Non-integer values are rounded to the nearest integer. |

`n2` |
total number of tags in second library.
Non-integer values are rounded to the nearest integer. |

### Details

SAGE is a method for counting the frequency of sequence tags in samples of RNA.
One can test for differential expression for a given tag between the SAGE results for two different RNA samples using Fisher's exact test.
This is however computationally intensive when the SAGE libraries are large.

This function uses a binomial approximation to the Fisher Exact test for each tag.
The approximation is accurate when `n1`

and `n2`

are large and `x`

and `y`

are small in comparison.

### Value

Numeric vector of p-values.

### Author(s)

Gordon Smyth

### References

http://www.sagenet.org

### See Also

`fisher.test`

### Examples

sage.test(c(0,5,10),c(0,30,50),n1=10000,n2=15000)
# Exact equivalents
fisher.test(matrix(c(0,0,10000-0,15000-0),2,2))$p.value
fisher.test(matrix(c(5,30,10000-5,15000-30),2,2))$p.value
fisher.test(matrix(c(10,50,10000-10,15000-50),2,2))$p.value

[Package

*statmod* version 1.2.4

Index]