Mercurial > repos > proteomisc > preprocess_dataset
annotate preprocess_datasets/Affymetrix_Preprocessing.R @ 46:31f89047724f draft default tip
Uploaded
| author | proteomisc |
|---|---|
| date | Mon, 29 Jan 2024 09:34:13 +0000 (21 months ago) |
| parents | 8aaf6fdb06d6 |
| children |
| rev | line source |
|---|---|
| 41 | 1 options(show.error.messages=F,warn=-1, error=function(){cat(geterrmessage(),file=stderr());q("no",1,F)}) |
| 2 sink(stdout(), type = "message") | |
| 3 sink(stdout() ,type = "output") | |
| 4 suppressWarnings(suppressMessages(library(affy))) | |
| 5 suppressWarnings(suppressMessages(library(affyPLM))) | |
| 6 suppressWarnings(suppressMessages(library(batch))) | |
| 7 suppressWarnings(suppressMessages(library(annotate))) | |
| 8 suppressWarnings(suppressMessages(library(limma))) | |
| 9 suppressWarnings(suppressMessages(library(markdown))) | |
| 10 suppressWarnings(suppressMessages(library(knitr))) | |
| 11 source_local <- function(fname){ | |
| 12 argv <- commandArgs(trailingOnly = FALSE) | |
| 13 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) | |
| 14 source(paste(base_dir, fname, sep="/")) | |
| 15 } | |
| 16 file_path <- function(fname){ | |
| 17 argv <- commandArgs(trailingOnly = FALSE) | |
| 18 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) | |
| 19 pato <- paste(base_dir, fname, sep="/") | |
| 20 return(pato) | |
| 21 } | |
| 22 base_dir <- function(){ | |
| 23 argv <- commandArgs(trailingOnly = FALSE) | |
| 24 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) | |
| 25 return(base_dir) | |
| 26 } | |
| 27 source_local("Affymetrix_Preprocessing_Functions.R") | |
| 28 listArguments = parseCommandArgs(evaluate=FALSE) | |
| 29 thefunctions=listArguments[["thefunctions"]] | |
| 30 listArguments[["thefunctions"]]=NULL | |
| 31 h=listArguments[["h"]] | |
| 32 listArguments[["h"]]=NULL | |
| 33 w=listArguments[["w"]] | |
| 34 listArguments[["w"]]=NULL | |
| 35 if (!is.null(listArguments[["image"]])){ | |
| 36 load(listArguments[["image"]]) | |
| 37 listArguments[["image"]]=NULL | |
| 38 } | |
| 39 listArguments[["rawdata"]]=MicroArray_Object$affy_object | |
| 40 if(datasetsource=="intern"){ | |
| 41 designo<-MicroArray_Object$designo | |
| 42 } | |
| 43 | |
| 44 if(datasetsource=="extern"){ | |
| 45 listArguments<-append(listArguments,list(datasetsource=datasetsource,listfullnames=listfullnames)) | |
| 46 } | |
| 47 Prepro_object<-do.call(thefunctions,listArguments) | |
| 48 if(datasetsource=="extern"){ | |
| 49 rownames(Prepro_object$data.bg@phenoData@data)<-listfullnames | |
| 50 colnames(exprs(Prepro_object$data.bg))<-listfullnames | |
| 51 colnames(exprs(Prepro_object$data.sm))<-listfullnames | |
| 52 colnames(exprs(Prepro_object$data.norm))<-listfullnames | |
| 53 colnames(exprs(Prepro_object$data.bg))<-listfullnames | |
| 54 colnames(exprs(Prepro_object$data.norm))<-listfullnames | |
| 55 rownames(Prepro_object$data.norm@phenoData@data)<-listfullnames | |
| 56 rownames(Prepro_object$data.norm@protocolData@data)<-listfullnames | |
| 57 } | |
| 58 | |
| 59 png(filename ="boxplot_before_NM.png",width = w, height = h, units = "px", pointsize = 14, bg = "white") | |
| 60 boxplot((na.omit(as.data.frame(exprs(Prepro_object$data.bg)))), main="Boxplot of intensities before Normalization",col="red",las=2,mar=c(15,2,1,1)) | |
| 61 invisible(dev.off()) | |
| 62 | |
| 63 png(filename ="boxplot_after_NM.png",width = w, height = h, units = "px", pointsize = 14, bg = "white") | |
| 64 boxplot((na.omit(as.data.frame(exprs(Prepro_object$data.sm)))), main="Boxplot of intensities After Normalization",col="red",ylab="(intensities)",las=2,mar=c(15,2,1,1)) | |
| 65 invisible(dev.off()) | |
| 66 | |
| 67 png(filename ="MA_plot.png",width = w, height = h) | |
| 68 MAplot((Prepro_object$data.norm) , | |
| 69 show.statistics = F, span = 2/3, family.loess = "gaussian", | |
| 70 cex = 2, plot.method = as.character("smoothScatter"), | |
| 71 azdd.loess = TRUE, lwd = 1, lty = 1, loess.col = "red") | |
| 72 | |
| 73 invisible(dev.off()) | |
| 74 | |
| 75 png(filename = "densities_plot_before_NM.png",width = w, height = h) | |
| 76 plotDensities(exprs(Prepro_object$data.bg),log=T) | |
| 77 invisible(dev.off()) | |
| 78 | |
| 79 png(filename = "densities_plot_after_NM.png",width = w, height = h) | |
| 80 plotDensities(exprs(Prepro_object$data.norm),log=T) | |
| 81 invisible(dev.off()) | |
| 82 | |
| 83 AffymetrixRmd=file_path("Affymetrix.Rmd") | |
| 84 Style=file_path("look.css") | |
| 85 suppressWarnings(suppressMessages(knit2html(AffymetrixRmd,output="PreprocessingPlots.html",quiet = T))) | |
| 86 #suppressWarnings(suppressMessages(markdownToHTML(AffymetrixRmd,output="PreprocessingPlots.html", stylesheet=Style))) | |
| 87 #suppressWarnings(suppressMessages(knit2html(AffymetrixRmd,output="PreprocessingPlots.html",quiet = T))) | |
| 88 rm(listArguments) | |
| 89 save.image("MicroArray.Preprocessing.RData") | |
| 90 sink() | |
| 91 sink() |