transform lfq data using robscale, vsn or log2, Assumes that data is not transformed (still needs log2 transformation)

It will also run internal but then robscale must be used.

Usage

transform_lfqdata(
  lfqdata,
  method = c("robscale", "vsn", "none", "log2"),
  internal = NULL
)

Arguments

lfqdata: LFQData
method: normalization method to use
internal: a data.frame with protein ids to be used for internal calibration, column name must be the same as

Examples

istar <- prolfqua::prolfqua_data('data_ionstar')$filtered()
#> Column added : nr_peptide_Id_IN_protein_Id
config <- prolfqua:::old2new(istar$config)
tmp <- prolfqua::LFQData$new(istar$data, config)
d <- istar$d
internal <- dplyr::filter(d, protein_Id %in% sample(unique(d$protein_Id), 3 )) |>
  dplyr::select(all_of(tmp$config$hierarchy_keys()[1])) |> dplyr::distinct()
tmp2 <- transform_lfqdata(tmp, internal = internal)
#> INFO [2026-02-25 16:36:17] Transforming using robscale.
#> Column added : log2_peptide.intensity
#> data is : TRUE
#> Warning: Expected 2 pieces. Additional pieces discarded in 25780 rows [1, 2, 3, 4, 5, 6,
#> 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, ...].
#> Joining with `by = join_by(protein_Id, sampleName, peptide_Id)`
#> INFO [2026-02-25 16:36:18] Transforming using robscale,
#> INFO [2026-02-25 16:36:18] Transforming Attempt of internal calibration.
#> Joining with `by = join_by(protein_Id)`
#> Column added : log2_peptide.intensity
#> Column added : log2_peptide.intensity
#> data is : TRUE
#> Warning: Expected 2 pieces. Additional pieces discarded in 25780 rows [1, 2, 3, 4, 5, 6,
#> 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, ...].
#> Joining with `by = join_by(protein_Id, sampleName, peptide_Id)`
#> INFO [2026-02-25 16:36:18] Transforming data : robscale.
tmp2 <- transform_lfqdata(tmp)
#> INFO [2026-02-25 16:36:18] Transforming using robscale.
#> Column added : log2_peptide.intensity
#> data is : TRUE
#> Warning: Expected 2 pieces. Additional pieces discarded in 25780 rows [1, 2, 3, 4, 5, 6,
#> 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, ...].
#> Joining with `by = join_by(protein_Id, sampleName, peptide_Id)`
#> INFO [2026-02-25 16:36:19] Transforming data : robscale.