#---example 1: Meta analysis of Differentially expressed genes between two classes----------#
# here I generate two pseudo datasets
label1<-rep(0:1,each=5)
label2<-rep(0:1,each=5)
exp1<-cbind(matrix(rnorm(5*20),20,5),matrix(rnorm(5*20,2),20,5))
exp2<-cbind(matrix(rnorm(5*20),20,5),matrix(rnorm(5*20,1.5),20,5))
#the input has to be arranged in lists
x<-list(list(exp1,label1),list(exp2,label2))
#here I used the modt test for individual study and used Fisher's method to combine results
#from multiple studies.
meta.res1<-MetaDE.rawdata(x=x,ind.method=c('modt','modt'),meta.method='Fisher',nperm=20)
#------example 2: genes associated with survival-----------#
# here I generate two pseudo datasets
exp1<-cbind(matrix(rnorm(5*20),20,5),matrix(rnorm(5*20,2),20,5))
time1=c(4,3,1,1,2,2,3,10,5,4)
event1=c(1,1,1,0,1,1,0,0,0,1)
exp2<-cbind(matrix(rnorm(5*20),20,5),matrix(rnorm(5*20,1.5),20,4))
time2=c(4,30,1,10,2,12,3,10,50)
event2=c(0,1,1,0,0,1,0,1,0)
#again,the input has to be arranged in lists
test2 <-list(list(x=exp1,y=time1,censoring.status=event1),list(x=exp2,y=time2,censoring.status=event2))
#here I used the log-rank test for individual study and used Fisher's method to combine results
#from multiple studies.
meta.res2<-MetaDE.rawdata(x=test2,ind.method=c('logrank','logrank'),meta.method='Fisher',nperm=20)
#------example 3: Fixed effect model for two studies from paired design-----------#
label1<-rep(0:1,each=5)
label2<-rep(0:1,each=5)
exp1<-cbind(matrix(rnorm(5*20),20,5),matrix(rnorm(5*20,2),20,5))
exp2<-cbind(matrix(rnorm(5*20),20,5),matrix(rnorm(5*20,1.5),20,5))
x<-list(list(x=exp1,y=label1),list(x=exp2,y=label2))
test<- MetaDE.rawdata(x,nperm=1000, meta.method="FEM", paired=rep(FALSE,2))
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