normalize_vsn {DEP} | R Documentation |
normalize_vsn
performs variance stabilizing transformation
using the vsn-package
.
normalize_vsn(se)
se |
SummarizedExperiment,
Proteomics data (output from |
A normalized SummarizedExperiment object.
# Load example data <- UbiLength data <- data[data$Reverse != "+" & data$Potential.contaminant != "+",] data_unique <- make_unique(data, "Gene.names", "Protein.IDs", delim = ";") # Make SummarizedExperiment columns <- grep("LFQ.", colnames(data_unique)) exp_design <- UbiLength_ExpDesign se <- make_se(data_unique, columns, exp_design) # Filter and normalize filt <- filter_missval(se, thr = 0) norm <- normalize_vsn(filt)