Normal.PBMC.MH450.Beta.R
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library("GEOquery") # PBMC-111 samples load("/home/shg047/oasis/monod/GEO/GSE53045_matrix.Rdata") GSE53045Beta <- as.data.frame(exprs(GSE530451)) phen <- pData(phenoData(GSE530451)) GSE53045NormalPBMC<-GSE53045Beta dim(GSE53045NormalPBMC) # PBMC-60 samples load("/home/shg047/oasis/monod/GEO/GSE35069_matrix.Rdata") GSE35069Beta <- as.data.frame(exprs(GSE350691)) phen <- pData(phenoData(GSE350691)) GSE35069NormalPBMC<-GSE35069Beta dim(GSE35069NormalPBMC) # PBMC-20 samples load("/home/shg047/oasis/monod/GEO/GSE32148_matrix.Rdata") GSE32148Beta <- as.data.frame(exprs(GSE321481)) phen <- pData(phenoData(GSE321481)) GSE32148NormalPBMC<-GSE32148Beta[,which(phen$description=="Normal peripheral blood sample")] dim(GSE32148NormalPBMC) # PBMC-192 load("/home/shg047/oasis/monod/GEO/GSE36054_matrix.Rdata") GSE36054Beta <- (exprs(GSE360541)) GSE36054Beta <- as.data.frame(GSE36054Beta) phen <- pData(phenoData(GSE360541)) GSE36054NormalPBMC<-GSE36054Beta dim(GSE36054NormalPBMC) # PBMC-78 load("/home/shg047/oasis/monod/GEO/GSE36064_matrix.Rdata") GSE36064Beta <- as.data.frame(exprs(GSE360641)) phen <- pData(phenoData(GSE360641)) GSE36064NormalPBMC<-GSE36064Beta dim(GSE36064NormalPBMC) # PBMC-689 load("/home/shg047/oasis/monod/GEO/GSE42861_matrix.Rdata") GSE42861Beta <- as.data.frame(exprs(GSE428611)) phen <- pData(phenoData(GSE428611)) GSE42861NormalPBMC<-GSE42861Beta[,which(phen$characteristics_ch1.1=="disease state: Normal")] dim(GSE42861NormalPBMC) data<-cbind(GSE53045NormalPBMC,GSE35069NormalPBMC,GSE32148NormalPBMC,GSE36054NormalPBMC,GSE36064NormalPBMC,GSE42861NormalPBMC) tmp<-t(apply(data,1,function(x) c(cpg=rownames(x),mean=mean(x,na.rm=T), median=median(x,na.rm=T), SD=sd(x,na.rm=T), Quantile=quantile(x,na.rm=T), SampleSize=length(na.omit(x)) ) ) ) write.table(tmp,file="Normal.PBMC.GEO.HM450K.Beta.txt",col.names=NA,row.names=T,sep="\t",quote=F)