library(sva) library(limma) setwd("C:\\Users\\Administrator\\Desktop\\06.batchNormalize") rt=read.table("merge.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(1,19),rep(2,20),rep(3,20)) modType=c(rep("normal",9),rep("OA",10),rep("normal",10),rep("OA",10),rep("normal",10),rep("OA",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)