regress: Run regression to fit genewise linear model

Description

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

Usage

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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

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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