do_eigenms_norm <-
function(data_m,classlabels,featselmethod=NA,feature_id_vector=NA,pairedanalysis=FALSE){
cnames_1<-colnames(classlabels)
if(dim(classlabels)[2]>2){
if(is.na(featselmethod)==FALSE){
if(featselmethod=="limma2way" | featselmethod=="limma2wayrepeat" | featselmethod=="lm2wayanova" | featselmethod=="lm2wayanovarepeat"){
if(pairedanalysis==FALSE){
treatment_vec<-as.factor(paste(classlabels[,2],":",classlabels[,3],sep=""))
}else{
treatment_vec<-as.factor(paste(classlabels[,3],":",classlabels[,4],sep=""))
}
}else{
if(featselmethod=="limma1way" | featselmethod=="limma1wayrepeat" | featselmethod=="lm1wayanova" | featselmethod=="lm1wayanovarepeat"){
check_factor2<-grep(cnames_1,pattern="Factor1")
if(pairedanalysis==FALSE){
treatment_vec<-as.factor(classlabels[,2])
}else{
treatment_vec<-as.factor(classlabels[,3])
}
}else{
treatment_vec<-as.factor(classlabels[,2])
}
#treatment_vec<-as.factor(classlabels[,2])
}
}else{
treatment_vec<-as.factor(classlabels[,2])
}
}else{
treatment_vec<-as.factor(classlabels[,2])
}
edata<-data_m #log2(data_m+1)
edata<-as.matrix(edata)
#save(edata,treatment_vec,feature_id_vector,file="testeig.Rda")
set.seed(123)
if(is.na(feature_id_vector)==FALSE){
ints_eig1 = eig_norm1(m=edata, treatment=treatment_vec, prot.info=cbind(paste('ID_',seq(1:nrow(data_m)), sep=''),feature_id_vector))
}else{
ints_eig1 = eig_norm1(m=edata, treatment=treatment_vec, prot.info=cbind(paste('ID_',seq(1:nrow(data_m)), sep=''),seq(1:nrow(data_m))))
}
set.seed(123)
data_m = eig_norm2(rv=ints_eig1)
data_m = data_m$norm_m
return(data_m)
}
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