make.contrast: Create a contrast matrix
In AffyExpress: Affymetrix Quality Assessment and Analysis Tool

Description Usage Arguments Value Author(s) See Also Examples

Create a contrast matrix based on a given design matrix

1 2	make.contrast(design.matrix, compare1=NULL, compare2=NULL, level=NULL, interaction=FALSE)

`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

contrast matrix for the linear model

Xiwei Wu xwu@coh.org, Xuejun Arthur Li xueli@coh.org

make.design

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")

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