Normalize MS data

Normalize MS data

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)
#> INFO  [2021-07-05 20:05:27] ** Features with one or two measurements across runs are removed.
#> INFO  [2021-07-05 20:05:27] ** Fractionation handled.
#> INFO  [2021-07-05 20:05:27] ** Updated quantification data to make balanced design. Missing values are marked by NA
input = MSstatsNormalize(input, "EQUALIZEMEDIANS") # median normalization
head(input)
#>    PROTEIN                      PEPTIDE TRANSITION
#> 1:  bovine             D.GPLTGTYR_23_23      NA_NA
#> 2:  bovine F.HFHWGSSDDQGSEHTVDR_402_402      NA_NA
#> 3:  bovine   F.HWGSSDDQGSEHTVDR_229_229      NA_NA
#> 4:  bovine                G.PLTGTYR_8_8      NA_NA
#> 5:  bovine       H.SFNVEYDDSQDK_465_465      NA_NA
#> 6:  bovine        K.AVVQDPALKPL_156_156      NA_NA
#>                               FEATURE LABEL GROUP_ORIGINAL SUBJECT_ORIGINAL RUN
#> 1:             D.GPLTGTYR_23_23_NA_NA     L             C1                1   1
#> 2: F.HFHWGSSDDQGSEHTVDR_402_402_NA_NA     L             C1                1   1
#> 3:   F.HWGSSDDQGSEHTVDR_229_229_NA_NA     L             C1                1   1
#> 4:                G.PLTGTYR_8_8_NA_NA     L             C1                1   1
#> 5:       H.SFNVEYDDSQDK_465_465_NA_NA     L             C1                1   1
#> 6:        K.AVVQDPALKPL_156_156_NA_NA     L             C1                1   1
#>    GROUP SUBJECT FRACTION INTENSITY ABUNDANCE originalRUN
#> 1:     1       1        1  757400.1  19.83052           1
#> 2:     1       1        1 2087125.8  21.29291           1
#> 3:     1       1        1 1485145.8  20.80200           1
#> 4:     1       1        1 4986404.0  22.54939           1
#> 5:     1       1        1 2488141.2  21.54646           1
#> 6:     1       1        1 7519322.0  23.14200           1