Mercurial > repos > proteomisc > preprocess_dataset

comparison preprocess_datasets/Affymetrix_Preprocessing.R @ 24:adbd4545d00d draft

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author proteomisc
date Mon, 04 Dec 2023 10:56:24 +0000
parents 2f468dd9ea39
children
comparison
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23:c0cc4bdf07af 24:adbd4545d00d
53 colnames(exprs(Prepro_object$data.bg))<-listfullnames 53 colnames(exprs(Prepro_object$data.bg))<-listfullnames
54 colnames(exprs(Prepro_object$data.norm))<-listfullnames 54 colnames(exprs(Prepro_object$data.norm))<-listfullnames
55 rownames(Prepro_object$data.norm@phenoData@data)<-listfullnames 55 rownames(Prepro_object$data.norm@phenoData@data)<-listfullnames
56 rownames(Prepro_object$data.norm@protocolData@data)<-listfullnames 56 rownames(Prepro_object$data.norm@protocolData@data)<-listfullnames
57 } 57 }
58 par(las=2,mar=c(15,2,1,1)) 58
59 png(filename ="boxplot_before_NM.png",width = w, height = h, units = "px", pointsize = 14, bg = "white") 59 png(filename ="boxplot_before_NM.png",width = w, height = h, units = "px", pointsize = 14, bg = "white")
60 par(las=2,mar=c(15,2,1,1))
61 boxplot((na.omit(as.data.frame(exprs(Prepro_object$data.bg)))), main="Boxplot of intensities before Normalization",col="red",las=2,mar=c(15,2,1,1)) 60 boxplot((na.omit(as.data.frame(exprs(Prepro_object$data.bg)))), main="Boxplot of intensities before Normalization",col="red",las=2,mar=c(15,2,1,1))
62
63 dev.off() 61 dev.off()
64 62
63 png(filename ="boxplot_after_NM.png",width = w, height = h, units = "px", pointsize = 14, bg = "white")
64 boxplot((na.omit(as.data.frame(exprs(Prepro_object$data.sm)))), main="Boxplot of intensities After Normalization",col="red",ylab="(intensities)",las=2,mar=c(15,2,1,1))
65 dev.off()
65 66
66
67 par(las=2,mar=c(15,2,1,1))
68 png(filename ="boxplot_after_NM.png",width = w, height = h, units = "px", pointsize = 14, bg = "white")
69 par(las=2,mar=c(15,2,1,1))
70 boxplot((na.omit(as.data.frame(exprs(Prepro_object$data.sm)))), main="Boxplot of intensities After Normalization",col="red",ylab="(intensities)",las=2,mar=c(15,2,1,1))
71
72 dev.off()
73 png(filename ="MA_plot.png",width = w, height = h) 67 png(filename ="MA_plot.png",width = w, height = h)
74 MAplot((Prepro_object$data.norm) , 68 MAplot((Prepro_object$data.norm) ,
75 show.statistics = F, span = 2/3, family.loess = "gaussian", 69 show.statistics = F, span = 2/3, family.loess = "gaussian",
76 cex = 2, plot.method = as.character("smoothScatter"), 70 cex = 2, plot.method = as.character("smoothScatter"),
77 azdd.loess = TRUE, lwd = 1, lty = 1, loess.col = "red") 71 azdd.loess = TRUE, lwd = 1, lty = 1, loess.col = "red")
78 72
79 dev.off() 73 dev.off()
74
80 png(filename = "densities_plot_before_NM.png",width = w, height = h) 75 png(filename = "densities_plot_before_NM.png",width = w, height = h)
81 plotDensities(exprs(Prepro_object$data.bg),log=T) 76 plotDensities(exprs(Prepro_object$data.bg),log=T)
82 dev.off() 77 dev.off()
83 78
84 png(filename = "densities_plot_after_NM.png",width = w, height = h) 79 png(filename = "densities_plot_after_NM.png",width = w, height = h)
85 plotDensities(exprs(Prepro_object$data.norm),log=T) 80 plotDensities(exprs(Prepro_object$data.norm),log=T)
86 dev.off() 81 dev.off()
82
87 AffymetrixRmd=file_path("Affymetrix.Rmd") 83 AffymetrixRmd=file_path("Affymetrix.Rmd")
88 Style=file_path("look.css") 84 Style=file_path("look.css")
89 suppressWarnings(suppressMessages(knit2html(AffymetrixRmd,output="PreprocessingPlots.html",quiet = T))) 85 suppressWarnings(suppressMessages(markdownToHTML(OneColorRmd,output="PreprocessingPlots.html",quiet = T, stylesheet=Style)))
86 #suppressWarnings(suppressMessages(knit2html(AffymetrixRmd,output="PreprocessingPlots.html",quiet = T)))
90 rm(listArguments) 87 rm(listArguments)
91 save.image("MicroArray.Preprocessing.RData") 88 save.image("MicroArray.Preprocessing.RData")
92 sink() 89 sink()
93 sink() 90 sink()