Normalize intensities across samples by dividing by the sample sum

Normalize across samples by dividing feature intensities by the sum of all intensities in a sample, making the sum 1 in all samples.

Important Note

Intensities of individual features will be very small after this normalization approach. It is therefore advised to multiply all intensities with a fixed number (e.g., 1000) after normalization. See this discussion on OMICSForum.ca and the examples below for further information.

Usage

normalize_sum(data)

Arguments

data

A tidy tibble created by read_featuretable.

Value

A tibble with intensities normalized across samples.

Examples

# Example 1: Normalization only
toy_metaboscape %>%
  normalize_sum()
#> # A tibble: 110 × 8
#>      UID Feature                Sample  Intensity    RT `m/z` Name       Formula
#>    <int> <chr>                  <chr>       <dbl> <dbl> <dbl> <chr>      <chr>  
#>  1     1 161.10519 Da 26.98 s   Sample1     0.138  0.45  162. NA         C7H15N…
#>  2     2 276.13647 Da 27.28 s   Sample1     0.103  0.45  277. Octyl hyd… C16H22…
#>  3     3 304.24023 Da 32.86 s   Sample1    NA      0.55  305. Arachidon… C20H32…
#>  4     4 417.23236 Da 60.08 s   Sample1     0.172  1     418. NA         NA     
#>  5     5 104.10753 Da 170.31 s  Sample1     0.172  2.84  105. NA         C5H14NO
#>  6     6 105.04259 Da 199.80 s  Sample1     0.172  3.33  106. NA         C3H8NO3
#>  7     7 237.09204 Da 313.24 s  Sample1    NA      5.22  238. Ketamine   C13H16…
#>  8     8 745.09111 Da 382.23 s  Sample1     0.103  6.37  746. NADPH      C21H30…
#>  9     9 427.02942 Da 424.84 s  Sample1     0.138  7.08  428. ADP        C10H15…
#> 10    10 1284.34904 Da 498.94 s Sample1    NA      8.32 1285. NA         NA     
#> # ℹ 100 more rows

# Example 2: Multiply with 1000 after normalization
toy_metaboscape %>%
  normalize_sum() %>%
  dplyr::mutate(Intensity = .data$Intensity * 1000)
#> # A tibble: 110 × 8
#>      UID Feature                Sample  Intensity    RT `m/z` Name       Formula
#>    <int> <chr>                  <chr>       <dbl> <dbl> <dbl> <chr>      <chr>  
#>  1     1 161.10519 Da 26.98 s   Sample1      138.  0.45  162. NA         C7H15N…
#>  2     2 276.13647 Da 27.28 s   Sample1      103.  0.45  277. Octyl hyd… C16H22…
#>  3     3 304.24023 Da 32.86 s   Sample1       NA   0.55  305. Arachidon… C20H32…
#>  4     4 417.23236 Da 60.08 s   Sample1      172.  1     418. NA         NA     
#>  5     5 104.10753 Da 170.31 s  Sample1      172.  2.84  105. NA         C5H14NO
#>  6     6 105.04259 Da 199.80 s  Sample1      172.  3.33  106. NA         C3H8NO3
#>  7     7 237.09204 Da 313.24 s  Sample1       NA   5.22  238. Ketamine   C13H16…
#>  8     8 745.09111 Da 382.23 s  Sample1      103.  6.37  746. NADPH      C21H30…
#>  9     9 427.02942 Da 424.84 s  Sample1      138.  7.08  428. ADP        C10H15…
#> 10    10 1284.34904 Da 498.94 s Sample1       NA   8.32 1285. NA         NA     
#> # ℹ 100 more rows