regress: Run regression to fit genewise linear model

In ArrayTools: geneChip Analysis Package

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)

ArrayTools documentation built on Nov. 8, 2020, 8:13 p.m.