# HG changeset patch
# User proteomisc
# Date 1701687384 0
# Node ID adbd4545d00da4176d89beaa8e2fe0ad085ab42d
# Parent  c0cc4bdf07afe7430f0b2d64e799f5d62511b3f9
Uploaded

diff -r c0cc4bdf07af -r adbd4545d00d preprocess_datasets/Affymetrix_Preprocessing.R
--- a/preprocess_datasets/Affymetrix_Preprocessing.R	Mon Dec 04 10:04:13 2023 +0000
+++ b/preprocess_datasets/Affymetrix_Preprocessing.R	Mon Dec 04 10:56:24 2023 +0000
@@ -55,21 +55,15 @@
 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()
 
-
+png(filename ="boxplot_after_NM.png",width = w, height = h, units = "px", pointsize = 14, bg = "white")
+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()
 
-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",
@@ -77,6 +71,7 @@
         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$data.bg),log=T)
 dev.off()
@@ -84,9 +79,11 @@
 png(filename = "densities_plot_after_NM.png",width = w, height = h)
 plotDensities(exprs(Prepro_object$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)))
+suppressWarnings(suppressMessages(markdownToHTML(OneColorRmd,output="PreprocessingPlots.html",quiet = T, stylesheet=Style)))
+#suppressWarnings(suppressMessages(knit2html(AffymetrixRmd,output="PreprocessingPlots.html",quiet = T)))
 rm(listArguments)
 save.image("MicroArray.Preprocessing.RData")
 sink()