one group is apparently bigger than other

9-microarray-examples/GSE21785.R

@@ -0,0 +1,47 @@
+## kidney	GPL96	HG-U133A
+## different subtype tissue :Glomerulus Tubulus
+rm(list=ls())
+library(GEOquery)
+library(limma) 
+GSE21785 <- getGEO('GSE21785', destdir=".",getGPL = F)
+exprSet=exprs(GSE21785[[1]])
+library("annotate")
+GSE21785[[1]]
+
+pdata=pData(GSE21785[[1]])
+tissue=factor(unlist(lapply(pdata$title,function(x) strsplit(as.character(x),"_")[[1]][1]))) 
+
+platformDB='hgu133a.db'
+library(platformDB, character.only=TRUE)
+probeset <- featureNames(GSE21785[[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)
+## very interesting here,one group is apparently bigger than other.
+
+design=model.matrix(~ tissue)
+fit=lmFit(exprSet,design)
+fit=eBayes(fit) 
+#vennDiagram(decideTests(fit))
+
+write.csv(topTable(fit,coef='tissueTubulus',n=Inf,adjust='BH'),"Tubulus-Glomerulus.DEG.csv")