Variance Stabilization Normalization of limma package.

Raw data should be taken as input (on_raw = TRUE).

Usage

vsnNorm(se, ain = "raw", aout = "VSN", on_raw = TRUE, VSN_quantile = 0.9)

Arguments

se

SummarizedExperiment containing all necessary information of the proteomic dataset

ain

String which assay should be used as input

aout

String which assay should be used to save normalized data

on_raw

Boolean specifying whether normalization should be performed on raw or log2-scaled data

VSN_quantile

Numeric of length 1. The quantile that is used for the resistant least trimmed sum of squares regression (see vsn2 lts.quantile)

Value

SummarizedExperiment containing the vsn normalized data as assay (on log2-scale)

See also

normalizeVSN()

Examples

data(tuberculosis_TMT_se)
tuberculosis_TMT_se <- vsnNorm(tuberculosis_TMT_se, ain = "raw",
                            aout = "VSN", on_raw = TRUE, VSN_quantile = 0.9)
#> Warning: 13 rows were removed since they contained only NA elements.