GPL96 // HG-U133A //obesity

9-microarray-examples/GSE474.R

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+## GPL96   HG-U133A 
+library(GEOquery)
+library(limma) 
+GSE474 <- getGEO('GSE474', destdir=".",getGPL = F)
+exprSet=exprs(GSE474[[1]])
+library("annotate")
+GSE474[[1]]
+pdata=pData(GSE474[[1]])
+status=factor(unlist(lapply(pdata$title,function(x) strsplit(as.character(x),"-")[[1]][3])))
+status=relevel(status,'NonObese') 
+
+platformDB='hgu133a.db'
+library(platformDB, character.only=TRUE)
+probeset <- featureNames(GSE474[[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(~ status)
+fit=lmFit(exprSet,design)
+fit=eBayes(fit) 
+vennDiagram(fit,include=c("up","down"))
+
+write.csv(topTable(fit,coef='statusMObese',n=Inf,adjust='BH'),"MObese-NonObese.DEG.csv")
+write.csv(topTable(fit,coef='statusObese',n=Inf,adjust='BH')  ,"Obese-NonObese.DEG.csv") 
+