Weighted Trimmed Mean of M Values (TMM) Normalization of edgeR package.

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

Usage

tmmNorm(se, ain = "raw", aout = "TMM", on_raw = TRUE)

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

Value

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

See also

calcNormFactors()

Examples

data(tuberculosis_TMT_se)
tuberculosis_TMT_se <- tmmNorm(tuberculosis_TMT_se, ain = "raw",
                                  aout = "TMM", on_raw = TRUE)