
library(samr)
    
set.seed(3)

#Note: Please set the following directory as explaind in the below coment:
#setwd(dir="M:\\DirectoryName\\DirectoryName\\.....") # Set Directory where the file (jdata_AverageSpectrum.txt) is located in your computer

joindata <- read.table("jdata_BreastCancer_AverageSpectra.txt",sep="\t", header=TRUE) #name of the file
msdata <- joindata[,1:62]

d=list(x=t(msdata),y=joindata$Status, geneid=as.character(1:62),genenames=names(msdata),logged2=TRUE) 

samr.obj=samr(d, resp.type="Two class unpaired", nperms=200)
# samr.obj=samr(d, resp.type="Multiclass", nperms=200)
delta.table <- samr.compute.delta.table(samr.obj)
 
delta=   0.6586               #(delta.table) this is the value in delta.table (FDR <0.001)

samr.plot(samr.obj,delta)
siggenes.table<-samr.compute.siggenes.table(samr.obj,delta, d, delta.table)
siggenes.table