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27
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1 AffymetrixPreprocessingFunction<-function(rawdata,backgroundcorrection_method,normalization_method,summary_method,datasetsource="",listfullnames="")
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2 {
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3 colnames(exprs(rawdata))<-listfullnames
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4 data.bg<-bg.correct(rawdata, method=backgroundcorrection_method)
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5 data.norm<-normalize(data.bg, method=normalization_method)
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6 data.sm<-threestep(data.norm, background=F, normalize=F,summary.method=summary_method)
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7 data_matrix=exprs(data.sm)
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8 sampleNames(data.sm)<-listfullnames
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9 if(datasetsource=="extern"){
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10 colnames(data_matrix)<-listfullnames
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11 data.sm=ExpressionSet(data_matrix,phenoData=phenoData(data.sm),featureData=featureData(data.sm),
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12 experimentData=experimentData(data.sm),annotation=annotation(data.sm),protocolData=protocolData(data.sm))
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13 write.table(format(exprs(data.sm), justify="right"),sep="\t", quote=FALSE,
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14 row.names=T, col.names=T,file="Matrix.Data.tsv")
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15 }else{
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16 colnames(data_matrix)<-designo$sample
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17 data.sm=ExpressionSet(data_matrix,phenoData=phenoData(data.sm),featureData=featureData(data.sm),
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18 experimentData=experimentData(data.sm),annotation=annotation(data.sm),protocolData=protocolData(data.sm))
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19 write.table(format(exprs(data.sm), justify="right"),sep="\t", quote=FALSE,
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20 row.names=T, col.names=T,file="Matrix.Data.tsv")
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21 }
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22 installed<-as.data.frame(installed.packages())
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23 lbraries=paste(annotation(data.sm),"db",sep='.')
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24 if(!lbraries%in%installed$Package){
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25 suppressWarnings(suppressMessages(require("BiocManager", quietly = TRUE)))
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26 suppressMessages(suppressWarnings(BiocManager::install(lbraries[!lbraries%in%installed$Package])))}
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27
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28 suppressWarnings(suppressMessages(library(lbraries,character.only = TRUE)))
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29
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30 symbol<-getSYMBOL(rownames(exprs(data.sm)), annotation(data.sm))
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31 return(list(data.bg=data.bg,data.norm=data.norm,data.sm=data.sm,matrix_data=exprs(data.sm),symbol=symbol))
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32
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33 }
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