NASH//liver//GPL15207-GEO

9-microarray-examples/GSE59045.R

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+## NASH	liver	GPL15207	Affymetrix Human Gene Expression Array
+##  Patients were grouped according histology: 
+##  group I (<5% steatosis), group II (NAFLD, 30-50% steatosis) and group III (NASH).
+rm(list=ls())
+library(GEOquery)
+library(limma) 
+GSE59045 <- getGEO('GSE59045', destdir=".",getGPL = F)
+exprSet=exprs(GSE59045[[1]])
+library("annotate")
+GSE59045[[1]]
+
+pdata=pData(GSE59045[[1]])
+treatment=factor(c(rep('steatosis',6),rep('NAFLD',4),rep('NASH',5)) ) 
+treatment=relevel(treatment,'steatosis')
+
+#platformDB='hgu133plus2.db'
+#library(platformDB, character.only=TRUE)
+probeset <- featureNames(GSE59045[[1]])
+library(Biobase)
+library(GEOquery)
+#Download GPL file, put it in the current directory, and load it:
+gpl <- getGEO('GPL15207', destdir=".")
+colnames(Table(gpl)) ## [1] 41108    17
+head(Table(gpl)[,c(1,15,19)])  ## you need to check this , which column do you need 
+probe2symbol=Table(gpl)[,c(1,15)]
+
+symbol=probe2symbol[match(probeset,probe2symbol[,1]),2]
+
+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(~ treatment)
+fit=lmFit(exprSet,design)
+fit=eBayes(fit) 
+vennDiagram(decideTests(fit))
+
+write.csv(topTable(fit,coef='treatmentNASH',n=Inf,adjust='BH'),"NASH-steatosis.DEG.csv")
+write.csv(topTable(fit,coef='treatmentNAFLD',n=Inf,adjust='BH'),"NAFLD-steatosis.DEG.csv")