--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/preprocess_datasets/Affymetrix_Preprocessing.R	Sat Dec 02 14:15:26 2023 +0000
@@ -0,0 +1,93 @@
+options(show.error.messages=F, error=function(){cat(geterrmessage(),file=stderr());q("no",1,F)})
+sink(stdout(), type = "message")
+suppressWarnings(suppressMessages(library(affy)))
+suppressWarnings(suppressMessages(library(affyPLM)))
+suppressWarnings(suppressMessages(library(batch)))
+suppressWarnings(suppressMessages(library(annotate)))
+suppressWarnings(suppressMessages(library(limma)))
+suppressWarnings(suppressMessages(library(markdown)))
+suppressWarnings(suppressMessages(library(knitr)))
+suppressWarnings(suppressMessages(library(BiocInstaller)))
+source_local <- function(fname){
+    argv <- commandArgs(trailingOnly = FALSE)
+    base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
+    source(paste(base_dir, fname, sep="/"))
+}
+file_path <- function(fname){
+  argv <- commandArgs(trailingOnly = FALSE)
+  base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
+  pato <- paste(base_dir, fname, sep="/")
+  return(pato)
+}
+base_dir <- function(){
+  argv <- commandArgs(trailingOnly = FALSE)
+  base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
+  return(base_dir)
+}
+source_local("Affymetrix_Preprocessing_Functions.R")  
+listArguments = parseCommandArgs(evaluate=FALSE)
+thefunctions=listArguments[["thefunctions"]]
+listArguments[["thefunctions"]]=NULL
+h=listArguments[["h"]]
+listArguments[["h"]]=NULL
+w=listArguments[["w"]]
+listArguments[["w"]]=NULL
+if (!is.null(listArguments[["image"]])){
+    load(listArguments[["image"]])
+    listArguments[["image"]]=NULL
+}
+listArguments[["path"]]=""
+print(listArguments)
+listArguments[["rawdata"]]=MicroArray_Object$affy_object
+if(datasetsource=="intern"){
+designo<-MicroArray_Object$designo
+}
+
+if(datasetsource=="extern"){
+listArguments<-append(listArguments,list(datasetsource=datasetsource,listfullnames=listfullnames))
+}
+Prepro_object<-do.call(thefunctions,listArguments)
+if(datasetsource=="extern"){
+rownames(Prepro_object$data.bg@phenoData@data)<-listfullnames
+colnames(exprs(Prepro_object$data.bg))<-listfullnames
+colnames(exprs(Prepro_object$data.sm))<-listfullnames
+colnames(exprs(Prepro_object$data.norm))<-listfullnames
+colnames(exprs(Prepro_object$data.bg))<-listfullnames
+colnames(exprs(Prepro_object$data.norm))<-listfullnames
+rownames(Prepro_object$data.norm@phenoData@data)<-listfullnames
+rownames(Prepro_object$data.norm@protocolData@data)<-listfullnames
+}
+par(las=2,mar=c(15,2,1,1))
+png(filename ="boxplot_before_NM.png",width = w, height = h, units = "px", pointsize = 14, bg = "white")
+par(las=2,mar=c(15,2,1,1))
+boxplot((na.omit(as.data.frame(exprs(Prepro_object$data.bg)))), main="Boxplot of  intensities before Normalization",col="red",las=2,mar=c(15,2,1,1))
+
+dev.off()
+
+
+
+par(las=2,mar=c(15,2,1,1))
+png(filename ="boxplot_after_NM.png",width = w, height = h, units = "px", pointsize = 14, bg = "white")
+par(las=2,mar=c(15,2,1,1))
+boxplot((na.omit(as.data.frame(exprs(Prepro_object$data.sm)))), main="Boxplot of  intensities After Normalization",col="red",ylab="(intensities)",las=2,mar=c(15,2,1,1))
+
+dev.off()
+png(filename ="MA_plot.png",width = w, height = h)
+MAplot((Prepro_object$data.norm) ,
+        show.statistics = F, span = 2/3, family.loess = "gaussian",
+        cex = 2, plot.method = as.character("smoothScatter"),
+        azdd.loess = TRUE, lwd = 1, lty = 1, loess.col = "red")
+
+dev.off()
+png(filename = "densities_plot_before_NM.png",width = w, height = h)
+plotDensities(exprs(Prepro_object$data.bg),log=T)
+dev.off()
+
+png(filename = "densities_plot_after_NM.png",width = w, height = h)
+plotDensities(exprs(Prepro_object$data.norm),log=T)
+dev.off()
+AffymetrixRmd=file_path("Affymetrix.Rmd")
+Style=file_path("look.css")
+suppressWarnings(suppressMessages(knit2html(AffymetrixRmd,output="PreprocessingPlots.html",quiet = T, stylesheet=Style)))
+rm(listArguments)
+save.image("MicroArray.Preprocessing.RData")