Total Intensity Normalization

Intensities of each variable in a sample are divided with the sum of intensities of all variables in the sample and multiplied with the median or mean of sum of intensities of all variables in all samples. Raw data should be taken as input (on_raw = TRUE).

Usage

globalIntNorm(
  se,
  ain = "raw",
  aout = "GlobalMedian",
  type = "median",
  on_raw = TRUE
)

Arguments

se

SummarizedExperiment containing all necessary information of the proteomics data set

ain

String which assay should be used as input

aout

String which assay should be used to save normalized data

type

String whether to use median or mean to calculate the scaling factor

on_raw

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

Value

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

Examples

data(tuberculosis_TMT_se)
tuberculosis_TMT_se <- globalIntNorm(tuberculosis_TMT_se, ain = "raw",
                                           aout = "GlobalMedian",
                                           type = "median",
                                           on_raw = TRUE)