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1 make_design<-function(MA_matrix){
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2 matrix<-RG.MA(MA_matrix$dataNBA)
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3 colnames_matrix<-NULL
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4 tmp<-strsplit(colnames(MA_matrix$dataNBA),split=".",fixed = T)
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5 for(i in 1:ncol(MA_matrix$dataNBA)){
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6 colnames_matrix[i]<-paste(tmp[[i]][1],"R",sep=".")
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7
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8 # .Red intensity
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9 }
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10 i=1;
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11 for(j in (ncol(MA_matrix$dataNBA)+1):((ncol(MA_matrix$dataNBA)*2))){
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12
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13 colnames_matrix[j]<-paste(tmp[[i]][1],"G",sep=".")
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14 i<-i+1;
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15 # .Green intensity
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16 }
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17 matrix_data<-cbind(matrix$R,matrix$G)
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18 colnames(matrix_data)<-colnames_matrix
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19 rownames(matrix_data)<-rownames(MA_matrix$dataNBA)
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20 MA_matrix$matrix_data<-log2(matrix_data)
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21 groupe<-c(rep("case",ncol(matrix$R)),rep("control",ncol(matrix$G)))
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22 sample=colnames(matrix_data)
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23 designo<-data.frame(sample=sample,groupetype=rep(designo$group,2),group=groupe)
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24 MA_matrix$designo<-designo
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25 write.table(format(designo, justify="right"),sep="\t", quote=FALSE,
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26 row.names=T, col.names=T,file="design.txt")
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27 return(MA_matrix)
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28 }
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