normalize_vsn {DEP}R Documentation

Normalization using vsn

Description

normalize_vsn performs variance stabilizing transformation using the vsn-package.

Usage

normalize_vsn(se)

Arguments

se

SummarizedExperiment, Proteomics data (output from make_se() or make_se_parse()). It is adviced to first remove proteins with too many missing values using filter_missval().

Value

A normalized SummarizedExperiment object.

Examples

# 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)

[Package DEP version 1.15.0 Index]