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comparison preprocess_datasets/Make_matrix_two_channels.R @ 11:bdc430a41508 draft

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author proteomisc
date Sun, 03 Dec 2023 14:07:23 +0000
parents ebf6607b4e6a
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comparison
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10:09a8947f1031 11:bdc430a41508
1 make_design<-function(MA_matrix){
2 matrix<-RG.MA(MA_matrix$dataNBA)
3 colnames_matrix<-NULL
4 tmp<-strsplit(colnames(MA_matrix$dataNBA),split=".",fixed = T)
5 for(i in 1:ncol(MA_matrix$dataNBA)){
6 colnames_matrix[i]<-paste(tmp[[i]][1],"R",sep=".")
7
8 # .Red intensity
9 }
10 i=1;
11 for(j in (ncol(MA_matrix$dataNBA)+1):((ncol(MA_matrix$dataNBA)*2))){
12
13 colnames_matrix[j]<-paste(tmp[[i]][1],"G",sep=".")
14 i<-i+1;
15 # .Green intensity
16 }
17 matrix_data<-cbind(matrix$R,matrix$G)
18 colnames(matrix_data)<-colnames_matrix
19 rownames(matrix_data)<-rownames(MA_matrix$dataNBA)
20 MA_matrix$matrix_data<-log2(matrix_data)
21 groupe<-c(rep("case",ncol(matrix$R)),rep("control",ncol(matrix$G)))
22 sample=colnames(matrix_data)
23 designo<-data.frame(sample=sample,groupetype=rep(designo$group,2),group=groupe)
24 MA_matrix$designo<-designo
25 write.table(format(designo, justify="right"),sep="\t", quote=FALSE,
26 row.names=T, col.names=T,file="design.txt")
27 return(MA_matrix)
28 }