obesity(omental subcutaneous)

9-microarray-examples/GSE20950.R

@@ -0,0 +1,50 @@
+## obesity adipose	GPL570	HG-U133_Plus_2
+## different subtype tissue :omental subcutaneous
+## different reactive for insulin : resistant sensitive
+rm(list=ls())
+library(GEOquery)
+library(limma) 
+GSE20950 <- getGEO('GSE20950', destdir=".",getGPL = F)
+exprSet=exprs(GSE20950[[1]])
+library("annotate")
+GSE20950[[1]]
+
+pdata=pData(GSE20950[[1]])
+tissue=factor(unlist(lapply(pdata$title,function(x) strsplit(as.character(x)," ")[[1]][6])))
+insulin=factor(unlist(lapply(pdata$title,function(x) strsplit(as.character(x)," ")[[1]][2])))
+
+platformDB='hgu133plus2.db'
+library(platformDB, character.only=TRUE)
+probeset <- featureNames(GSE20950[[1]])
+#EGID <- as.numeric(lookUp(probeset, platformDB, "ENTREZID"))
+SYMBOL <-  lookUp(probeset, platformDB, "SYMBOL")
+
+a=cbind(SYMBOL,exprSet)
+## remove the duplicated probeset 
+rmDupID <-function(a=matrix(c(1,1:5,2,2:6,2,3:7),ncol=6)){
+  exprSet=a[,-1]
+  rowMeans=apply(exprSet,1,function(x) mean(as.numeric(x),na.rm=T))
+  a=a[order(rowMeans,decreasing=T),]
+  exprSet=a[!duplicated(a[,1]),]
+  #
+  exprSet=exprSet[!is.na(exprSet[,1]),]
+  rownames(exprSet)=exprSet[,1]
+  exprSet=exprSet[,-1]
+  return(exprSet)
+}
+exprSet=rmDupID(a)
+rn=rownames(exprSet)
+exprSet=apply(exprSet,2,as.numeric)
+rownames(exprSet)=rn
+exprSet[1:4,1:4]
+#exprSet=log(exprSet) ## based on e 
+boxplot(exprSet,las=2)
+
+design=model.matrix(~ tissue+insulin)
+fit=lmFit(exprSet,design)
+fit=eBayes(fit) 
+vennDiagram(fit,include=c("up","down"))
+
+write.csv(topTable(fit,coef='tissuesubcutaneous',n=Inf,adjust='BH'),"subcutaneous-omental.DEG.csv")
+write.csv(topTable(fit,coef='insulinsensitive',n=Inf,adjust='BH')  ,"sensitive-resistant.DEG.csv") 
+