In protViz/SRMService: Report Quantitative Mass Spectrometry Data

normalize using all housekeepers

prtable$heatmap()
prtable$conditionColors()
boxplot(prtable$data,las=2, main="normalized",pch="*")

normall <- prtable$normalize()
prtable$housekeeper
normall$housekeeper

normall$heatmap()
normall$normalized
boxplot(normall$data,las=2, main="normalized",pch="*")
write.csv(normall$getProteinMatrix(), file = paste("data/outputSRM/",normall$experimentID,"All.tsv",sep="" ))
saveRDS(normall,paste("data/outputSRM/",normall$experimentID,"All.rds",sep="" ))

for( i in 1:length(prtable$housekeeper) ){
  name <- prtable$housekeeper[i]
  if(sum(is.na(prtable$getProtein(name)))==0){
    norm <- prtable$normalize(name)
    norm$heatmap(name)
    boxplot(norm$data,las=2, main=name,pch="*")
    norm$data <- norm$data[!grepl(name,rownames(norm$data) ),]
    filename <- paste("data/outputSRM/",norm$experimentID,name,".tsv",sep="")
    write.csv(norm$getProteinMatrix(), filename )
    filename <- paste("data/outputSRM/",norm$experimentID,name,".rds",sep="")
    saveRDS(norm, file=filename)
  }
}