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 1.12.0 Index]