LimmaGuideCh7-8.R

Code snipits and programs written in R, S or S-PLUS

library(limma)

1. 7.2 Paired samples

design <- model.matrix(~ -1+factor(c(1,1,1,2,2,3,3,3))) colnames(design) <- c("group1", "group2", "group3") design

contrast.matrix <- makeContrasts(group2-group1, group3-group2, group3-group1, levels=design) contrast.matrix

1. 7.3

targets <- readTargets(file.path("/Volumes/HD2/R/Examples/limmaGuideData", "runxtargets.txt"), sep=" ") targets design <- modelMatrix(targets,ref="EGFP") design contrast.matrix <- makeContrasts(AML1,CBFb,AML1.CBFb,AML1.CBFb-AML1,AML1.CBFb-CBFb, levels=design) contrast.matrix

1. 7.4

targets <- read.csv(file=stdin(), sep=" ") SlideNumber FileName Cy3 Cy5 12 ml12med.spot CD4 CD8 13 ml13med.spot CD8 CD4 14 ml14med.spot DN CD8 15 ml15med.spot CD8 DN 16 ml16med.spot CD4 DN 17 ml17med.spot DN CD4 "" set.seed(1) rownames(targets) <- paste("rowInd ", LETTERS[sort(sample(26,6))], sep="") targets design <- modelMatrix(targets, ref="CD4") design

contrast.matrix <- cbind("CD8-CD4"=c(1,0),"DN-CD4"=c(0,1),"CD8-DN"=c(1,-1)) rownames(contrast.matrix) <- colnames(design) contrast.matrix

1. 8.1

targets <- data.frame(cbind(FileName=paste("File",1:3, sep=""), Cy3=c("wt","mu","wt"), Cy5=c("mu","wt","mu"))) targets

modelMatrix(targets, ref="wt")

1. 8.4

targets <- data.frame(cbind(FileName=paste("File",1:5, sep=""), Cy3=rep("Ref",5), Cy5=rep(c("WT","Mu"), c(2,3)))) targets design <- modelMatrix(targets, ref="Ref") design contr <- makeContrasts(MUvsWT=WT-Mu, levels=design) contr design %*% contr

1. Loop design example

design <- diag(5)[rep(1:5, each=2),] colnames(design) <- c("BtoA","CtoB","DtoC","EtoD","AtoE")

makeContrasts("B-A" = BtoA,

             "C-A" = CtoB - BtoA,
             "D-A" = DtoC - CtoB - BtoA,
             "E-A" = EtoD - DtoC - CtoB - BtoA,
             "E-A alternative" = AtoE,
             levels=design)