diff AffyQCnormalization.R @ 2:93451f832736 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/AffyQCnormalization.R	Tue Mar 21 10:28:47 2017 -0400
@@ -0,0 +1,110 @@
+library(Biobase)
+library(GEOquery)
+library(GEOmetadb)
+library(limma)
+library(jsonlite)
+library(affy)
+library(affyPLM)
+library(dplyr)
+
+cargs<-commandArgs()
+cargs<-cargs[(which(cargs=="--args")+1):length(cargs)]
+nbargs=length(cargs)
+celList=vector()
+celFileNameList=vector()
+for (i in seq(1,nbargs-7,2))
+{
+	celList=c(celList,cargs[[i]])
+	celFileNameList=c(celFileNameList,cargs[[i+1]])
+}
+
+
+normalization=cargs[[nbargs-6]]
+result_export_eset=cargs[[nbargs-5]]
+result=cargs[[nbargs-4]]
+result.path=cargs[[nbargs-3]]
+result.template=cargs[[nbargs-2]]
+
+dir.create(result.path, showWarnings = TRUE, recursive = TRUE)
+for(i in 1:length(celList))
+{
+	file.copy(celList[i],paste0("./",celFileNameList[i]))
+}
+
+data <- ReadAffy(filenames=celFileNameList, celfile.path=".")
+htmlfile=readChar(result.template, file.info(result.template)$size)
+
+boxplot="boxplot.png"
+png(boxplot,width=800,height = 400)
+par(mar=c(7,5,1,1))
+boxplot(data,las=2,outline=FALSE)
+dev.off()
+htmlfile=gsub(x=htmlfile,pattern = "###BOXPLOT###",replacement = boxplot, fixed = TRUE)
+file.copy(boxplot,result.path)
+
+images="images.png"
+nblines=length(celList)%/%4 + as.numeric((length(celList)%%4)!=0) 
+png(images,width=800,height = 200*nblines)
+par(mfrow=c(nblines,4))
+image(data)
+dev.off()
+htmlfile=gsub(x=htmlfile,pattern = "###IMAGES###",replacement = images, fixed = TRUE)
+file.copy(images,result.path)
+
+
+plotMA="plotMA.png"
+nblines=length(celList)%/%3 + as.numeric((length(celList)%%3)!=0) 
+png(plotMA,width=800,height =300*nblines )
+par(mfrow=c(nblines,3))
+MAplot(data)
+dev.off()
+htmlfile=gsub(x=htmlfile,pattern = "###PLOTMA###",replacement = plotMA, fixed = TRUE)
+file.copy(plotMA,result.path)
+
+
+if (normalization == "rma") {
+	eset <- rma(data)
+} else if (normalization == "quantile") {
+	eset = rma(data,background = FALSE,normalize = TRUE)
+} else if (normalization == "background"){
+	eset = rma(data,background = TRUE ,normalize = FALSE)
+} else if (normalization == "log2") {
+	eset = rma(data,background = FALSE ,normalize = FALSE)
+}
+	
+
+boxplotnorm="boxplotnorm.png"
+png(boxplotnorm,width=800,height = 400)
+par(mar=c(7,5,1,1))
+boxplot(data.frame(exprs(eset)),las=2,outline=FALSE)
+dev.off()
+htmlfile=gsub(x=htmlfile,pattern = "###BOXPLOTNORM###",replacement = boxplotnorm, fixed = TRUE)
+file.copy(boxplotnorm,result.path)
+
+plotMAnorm="plotMAnorm.png"
+nblines=length(celList)%/%3 + as.numeric((length(celList)%%3)!=0) 
+png(plotMAnorm,width=800,height =300*nblines )
+par(mfrow=c(nblines,3))
+#for (i in 1:length(celList)){
+MAplot(eset)
+#}
+
+dev.off()
+htmlfile=gsub(x=htmlfile,pattern = "###PLOTMANORM###",replacement = plotMAnorm, fixed = TRUE)
+file.copy(plotMAnorm,result.path)
+#write.table(tolower(c(condition1Name,condition2Name)),quote = FALSE,col.names = FALSE, row.names=FALSE,file=result_export_conditions)
+#saveConditions=c(condition1Name,condition2Name)
+save(eset,file=result_export_eset)
+write(htmlfile,result)
+
+#l=list()
+#for(i in 1:length(esets))
+#{
+#	l[[paste("study",i,sep="")]]<-res[[i]]
+#}
+#l[["Meta"]]=res[[length(res)-1]]
+#showVenn(res,file.path(temp.files.path,"venn.png"))
+#writeLines(c("<h2>Venn diagram</h2>"),file.conn)
+#writeLines(c("<img src='venn.png'><br/><br/>"),file.conn)
+#writeLines(c("</body></html>"),file.conn)
+#close(file.conn)
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