# HG changeset patch
# User proteomisc
# Date 1701687491 0
# Node ID 66aaf716040c36abf550feb4ac1201a5c8287a90
# Parent  adbd4545d00da4176d89beaa8e2fe0ad085ab42d
Uploaded

diff -r adbd4545d00d -r 66aaf716040c preprocess_datasets/Agilent_One_Color_Preprocessing.R
--- a/preprocess_datasets/Agilent_One_Color_Preprocessing.R	Mon Dec 04 10:56:24 2023 +0000
+++ b/preprocess_datasets/Agilent_One_Color_Preprocessing.R	Mon Dec 04 10:58:11 2023 +0000
@@ -52,24 +52,19 @@
 colnames(Prepro_object$dataNBA[[1]])<-listcelsnames[-1]
 Prepro_object$dataNBA[[2]]$FileName<-listfullnames
 }
-par(las=2,mar=c(15,2,1,1))
+
 png(filename ="boxplot_before_BG.png",width = w, height = h, units = "px", pointsize = 14, bg = "white")
 boxplot(log2(na.omit(as.data.frame(MicroArray_Object[[1]]$E))), main="Boxplot of log2( intensities) before Background Correction",col="red",ylab="log2( intensities)",xlab="",las=2,mar=c(15,2,1,1))
-
 dev.off()
 
 png(filename ="boxplot_after_BG.png",width = w, height = h, units = "px", pointsize = 14, bg = "white")
-
 boxplot(log2(na.omit(as.data.frame(Prepro_object$dataBG$E))), main="Boxplot of log2( intensities) After Background Correction",col="red",ylab="log2( intensities)",xlab="",las=2,mar=c(15,2,1,1))
-
 dev.off()
 
-
 png(filename ="boxplot_after_NBA.png",width = w, height = h, units = "px", pointsize = 14, bg = "white")
+boxplot(log2(na.omit(as.data.frame(Prepro_object$dataNBA$E))), main="Boxplot of log2( intensities) After Normalization Between Arrays",col="red",ylab="log2(R intensities)",xlab="",las=2,mar=c(15,2,1,1))
+dev.off()
 
-boxplot(log2(na.omit(as.data.frame(Prepro_object$dataNBA$E))), main="Boxplot of log2( intensities) After Normalization Between Arrays",col="red",ylab="log2(R intensities)",xlab="",las=2,mar=c(15,2,1,1))
-
-dev.off()
 png(filename = "densities_plot_before_BG.png",width = w, height = h)
 plotDensities(MicroArray_Object[[1]],log=T)
 dev.off()
@@ -82,8 +77,10 @@
 png(filename = "densities_plot_after_NBA.png",width = w, height = h)
 plotDensities(Prepro_object$dataNBA,log=T)
 dev.off()
+
 OneColorRmd=file_path("OneColor.Rmd")
 Style=file_path("look.css")
-suppressWarnings(suppressMessages(knit2html(OneColorRmd,output="PreprocessingPlots.html",quiet = T, stylesheet=Style)))
+suppressWarnings(suppressMessages(markdownToHTML(OneColorRmd,output="PreprocessingPlots.html",quiet = T, stylesheet=Style)))
+# suppressWarnings(suppressMessages(knit2html(OneColorRmd,output="PreprocessingPlots.html",quiet = T, stylesheet=Style)))
 rm(listArguments)
 save.image("MicroArray.Preprocessing.RData")