makeEBcontr: A function to make the contrast vectors needed for EBarrays

In Bioconductor/Category: Category Analysis

A function to make the contrast vectors needed for EBarrays

Description

Using EBarrays to detect differential expression requires the construction of a set of contrasts. This little helper function computes these contrasts for a two level factor.

Usage

makeEBcontr(f1, hival)

Arguments

f1	The factor that will define the contrasts.
hival	The level of the factor to treat as the high level.

Details

Not much more to add, see EBarrays for more details. This is used in the Category package to let users compute the posterior probability of differential expression, and hence to compute expected numbers of differentially expressed genes, per category.

Value

An object of class “ebarraysPatterns”.

Author(s)

R. Gentleman

See Also

ebPatterns

Examples

 if( require("EBarrays") ) {
  myfac = factor(rep(c("A", "B"), c(12, 24)))
  makeEBcontr(myfac, "B")
 }

Bioconductor/Category documentation built on Nov. 2, 2024, 6:33 a.m.