sage.test {statmod} | R Documentation |
Compute p-values for differential expression for each tag between two serial analysis of gene expression (SAGE) libraries.
sage.test(x, y, n1=sum(x), n2=sum(y))
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. |
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.
Numeric vector of p-values.
Gordon Smyth
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