regress {ArrayTools} | R Documentation |
Fit genewise linear model using LIMMA package, ordinary linear regression, or permutation method.
regress(object, contrast, method = c("limma", "regression", "permutation"), adj = "none", permute.time = 1000)
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 |
an object of regressResult
Xiwei Wu, Arthur Li
data(eSetExample) design<- new("designMatrix", target=pData(eSetExample), covariates = "Treatment") contrast<- new("contrastMatrix", design.matrix = design, compare1 = "Treated", compare2 = "Control") result<- regress(eSetExample, contrast)