regress {ArrayTools}R Documentation

Run regression to fit genewise linear model

Description

Fit genewise linear model using LIMMA package, ordinary linear regression, or permutation method.

Usage

regress(object, contrast, method = c("limma", "regression", "permutation"), adj = "none", permute.time = 1000)

Arguments

object an ExpressionSet
contrast a contrastMatrix
method choose the follwoing three options: "limma" (LIMMA), "regression" (ordinary linear regression), "permutation" (permutation test)
adj adjustment method for multiple comparison test, including "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none". The default value is "none". Type help(p.adjust) for more detail.
permute.time number of permutation times, only used for the "permutation" method

Value

an object of regressResult

Author(s)

Xiwei Wu, Arthur Li

Examples

data(eSetExample)
design<- new("designMatrix", target=pData(eSetExample), covariates = "Treatment")
contrast<- new("contrastMatrix", design.matrix = design, 
    compare1 = "Treated", compare2 = "Control")
result<- regress(eSetExample, contrast)

[Package ArrayTools version 1.2.1 Index]