Skeletal Muscle//GPL9486//Hs133P_Hs_ENST

9-microarray-examples/GSE18732.R

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+## Skeletal Muscle	GPL9486	Hs133P_Hs_ENST
+## different subtype tissue :Glomerulus Tubulus
+rm(list=ls())
+library(GEOquery)
+library(limma) 
+GSE18732 <- getGEO('GSE18732', destdir=".",getGPL = F)
+exprSet=exprs(GSE18732[[1]])
+library("annotate")
+GSE18732[[1]]
+
+pdata=pData(GSE18732[[1]])
+treatment=factor(unlist(lapply(pdata$title,function(x) strsplit(as.character(x),"[_ ]")[[1]][2]))) 
+treatment=relevel(treatment,'normal')
+table(treatment)
+#treatment
+#           normal          diabetic glucoseIntolerant 
+#               47                45                26 
+platformDB='hgu133plus2.db'
+library(platformDB, character.only=TRUE)
+probeset <- featureNames(GSE18732[[1]])
+ENST=sub("_at","",probeset)
+library(org.Hs.eg.db)
+ENST2ENG=toTable(org.Hs.egENSEMBLTRANS)
+EGID=ENST2ENG[match(ENST,ENST2ENG[,2]),1]
+
+a=cbind(EGID,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(~ treatment)
+fit=lmFit(exprSet,design)
+fit=eBayes(fit) 
+vennDiagram(decideTests(fit))
+
+write.csv(topTable(fit,coef='treatmentdiabetic',n=Inf,adjust='BH'),"diabetic-normal.DEG.csv")
+write.csv(topTable(fit,coef='treatmentglucoseIntolerant',n=Inf,adjust='BH'),"glucoseIntolerant-normal.DEG.csv")