## R code for analyzing Hedenfalk et al. (2001) data


brca <- matrix(scan("C:/Documents and Settings/School of Public Hea/Desktop/Research/MData/brca.txt",list(plate="",cid = 0,name="",BC11 = 0,BC15=0,BC13 = 0,BC17 = 0, BC12 = 0, BC14=0,BC210a = 0,BC29 = 0,BC28 = 0,BC210b = 0,SP16=0,SP17=0,SP15=0,SP18=0,SP19=0,SP21=0,SP20=0,BC16=0,BC213=0,BC214=0,BC211=0,BC212=0),sep="\t",skip=3)





brca <- data.frame(brca)
cid <- brca$cid
gn <- brca[,3]

brca <- (brca[,c(-1,-2,-3)])

brca <- as.matrix(brca)


library(e1071)
library(mda)
source("POSmacros.txt")

brca.class <- c(rep(1,6),rep(2,4),rep(0,7),1,rep(2,4))

# Fit a SVD-based discriminant analysis with K = 3 components

da1 <- svdrfda(factor(brca.class)~t(brca),K=3)

# Fit a PLS-based discriminant analysis with K = 5 components

da2 <- svdpls3fda(factor(brca.class)~t(brca),K=3)