sage.test

0th

Percentile

Compare Two SAGE Libraries

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

Keywords
htest
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.

References

http://www.sagenet.org

See Also

fisher.test

Aliases
  • sage.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
Documentation reproduced from package statmod, version 1.2.3, License: LGPL version 2 or newer

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