MSstatsNormalize {MSstats} | R Documentation

## Normalize MS data

### Description

Normalize MS data

### Usage

    MSstatsNormalize(
      input,
      normalization_method,
      peptides_dict = NULL,
      standards = NULL
    )

### Arguments

`input` | data.table in MSstats format
`normalization_method` | name of a chosen normalization method: "NONE" or "FALSE" for no normalization, "EQUALIZEMEDIANS" for median normalization, "QUANTILE" normalization for quantile normalization from 'preprocessCore' package, "GLOBALSTANDARDS" for normalization based on selected peptides or proteins.
`peptides_dict` | 'data.table' of names of peptides and their corresponding features.
`standards` | character vector with names of standards, required if "GLOBALSTANDARDS" method was selected.

### Value

data.table

### Examples

    raw = DDARawData
    method = "TMP"
    cens = "NA"
    impute = TRUE
    MSstatsConvert::MSstatsLogsSettings(FALSE)
    input = MSstatsPrepareForDataProcess(raw, 2, NULL)
    input = MSstatsNormalize(input, "EQUALIZEMEDIANS") # median normalization
    head(input)

[Package MSstats version 4.1.1 Index]