Mercurial > repos > proteomisc > preprocess_dataset

comparison preprocess_datasets/Affymetrix_Preprocessing.R @ 21:5d481ae1b76c draft

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Uploaded
author proteomisc
date Sun, 03 Dec 2023 17:08:48 +0000
parents d05e52d7904d
children 2f468dd9ea39
comparison
equal deleted inserted replaced
20:d05e52d7904d 21:5d481ae1b76c
1 options(show.error.messages=F, error=function(){cat(geterrmessage(),file=stderr());q("no",1,F)}) 1 options(show.error.messages=F,warn=-1, error=function(){cat(geterrmessage(),file=stderr());q("no",1,F)})
2 sink(stdout(), type = "message") 2 sink(stdout(), type = "message")
3 sink(stdout() ,type = "output")
3 suppressWarnings(suppressMessages(library(affy))) 4 suppressWarnings(suppressMessages(library(affy)))
4 suppressWarnings(suppressMessages(library(affyPLM))) 5 suppressWarnings(suppressMessages(library(affyPLM)))
5 suppressWarnings(suppressMessages(library(batch))) 6 suppressWarnings(suppressMessages(library(batch)))
6 suppressWarnings(suppressMessages(library(annotate))) 7 suppressWarnings(suppressMessages(library(annotate)))
7 suppressWarnings(suppressMessages(library(limma))) 8 suppressWarnings(suppressMessages(library(limma)))
86 AffymetrixRmd=file_path("Affymetrix.Rmd") 87 AffymetrixRmd=file_path("Affymetrix.Rmd")
87 Style=file_path("look.css") 88 Style=file_path("look.css")
88 suppressWarnings(suppressMessages(knit2html(AffymetrixRmd,output="PreprocessingPlots.html",quiet = T, stylesheet=Style))) 89 suppressWarnings(suppressMessages(knit2html(AffymetrixRmd,output="PreprocessingPlots.html",quiet = T, stylesheet=Style)))
89 rm(listArguments) 90 rm(listArguments)
90 save.image("MicroArray.Preprocessing.RData") 91 save.image("MicroArray.Preprocessing.RData")
92 sink()
93 sink()