AffyExpress (version 1.38.0)

make.contrast: Create a contrast matrix

Description

Create a contrast matrix based on a given design matrix

Usage

make.contrast(design.matrix, compare1=NULL, compare2=NULL, level=NULL,  interaction=FALSE)

Arguments

design.matrix

a design matrix returned from the make.design funcion

compare1

the first value of the main covariate. For example, suppose that the main covariate is "drug", and there are three unique values: "drug1", "drug2", and "placebo". You would like to compare "drug1" to "drug2". Then you would use "drug1" as compare1. If interaction==TRUE, do not specify this value.

compare2

the second value of the main covariate. Based on the example above, if you would like to compare "drug1" vs "drug2", then you would use "drug2" as compare2. If interaction ==TRUE, do not specify this value

level

you only specify this term when the design matrix contains an interaction term. Suppose that you would like to compare "drug1" to "drug2" only when estrogen is "present", where "present" is one of the values of the estrogen variable. You will use "present" as level. If interaction==TRUE, do not specify this value

interaction

you only specify interaction=TRUE when you would like to detect the interaction effect between two covariates. When you specify interaction=TRUE, do not provide values for compare1, compare2, and level

Value

contrast matrix for the linear model

See Also

make.design

Examples

target<-data.frame(drug=(c(rep("A",4),rep("B",4),rep("C",4))), 
gender=factor(c(rep("M",6),rep("F",6))), 
group=factor(rep(c(1,2,3),4)))

# Example1:  Compare drug "A" vs. "B"
design1<-make.design(target, "drug")
contrast1<-make.contrast(design1, "A", "B")

# Example2:  Compare drug "A" vs. "B", adjusting for "group" variable
design2<-make.design(target, c("drug","group"))
contrast2<-make.contrast(design2, "A", "B")

# Example3:  Suppose you are interested in "drug", "group" interaction
design3<-make.design(target, c("drug","group"), int=c(1,2))
contrast3<-make.contrast(design3, interaction=TRUE)

# Example4:  Compare drug "A" vs. "B" among "male"
# Notice that you must use an design matrix containing an interaction term
design4<-make.design(target, c("drug","gender"), int=c(1,2))
contrast4<-make.contrast(design4, "A", "B", "M")