Mercurial > repos > proteomisc > preprocess_dataset
changeset 38:3277861975eb draft
Uploaded
| author | proteomisc |
|---|---|
| date | Sat, 16 Dec 2023 12:23:16 +0000 |
| parents | 10acbb8418d7 |
| children | e80d3d455db7 |
| files | preprocess_datasets/Agilent_One_Color_Preprocessing_Functions.R |
| diffstat | 1 files changed, 18 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/preprocess_datasets/Agilent_One_Color_Preprocessing_Functions.R Sat Dec 16 12:23:16 2023 +0000 @@ -0,0 +1,18 @@ +AgilentOneColorPreprocessingFunction<- function(data,methodBC,methodNBA) +{ +MA <<- backgroundCorrect(data, method=methodBC ,offset = 2) +rownames(MA$E)=MA$genes$ProbeName +MA<-MA[rm.na(rownames(MA$E)),] +MAb <<-suppressWarnings(suppressMessages(normalizeBetweenArrays(MA, method=methodNBA))) +data_mt<-NaRV.omit(as.data.frame(MAb$E)) +MAb$E=(data_mt) +MAb$genes=MAb$genes[(MAb$genes$ProbeName %in% rownames(MAb$E)),] +MAb$E=MAb$E[rownames(MAb$E) %in% MAb$genes$ProbeName,] +MA.avg <-suppressWarnings(suppressMessages(avereps(MAb, ID=rownames(MAb$E)))) +data_matrix=NaRV.omit(MA.avg$E) +colnames(data_matrix)<-designo$sample +write.table(format(data_matrix, justify="right"),sep="\t", quote=FALSE, + row.names=T, col.names=T,file="Matrix.Data.tsv") + +return(list(dataNBA=MA.avg,dataBG=MA,matrix_data=as.matrix(MA.avg$E),symbol=MA.avg$genes$GeneName)) +}