if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install("limma", version = "3.8")
if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install("sva", version = "3.8")

library(sva)
library(limma)
setwd("D:\\Bioinformatics\\WGCNA\\Bacth normalization")
rt=read.table("merge2.txt",sep="\t",header=T,check.names=F)
rt=as.matrix(rt)
rownames(rt)=rt[,1]
exp=rt[,2:ncol(rt)]
dimnames=list(rownames(exp),colnames(exp))
data=matrix(as.numeric(as.matrix(exp)),nrow=nrow(exp),dimnames=dimnames)  
batchType=c(rep(1,15),rep(2,22),rep(3,59)) 
modType=c(rep("AAA",7),rep("Normal",8),rep("AAA",14),rep("Normal",8),rep("AAA",49),rep("Normal",10)) 
mod = model.matrix(~as.factor(modType))
outTab=ComBat(data, batchType, mod, par.prior=TRUE)
outTab=rbind(geneNames=colnames(outTab),outTab)
write.table(outTab,file="normalize.txt",sep="\t",quote=F,col.names=F)