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]