Skip to contents

Cyclic Linear Regression Normalization on MA Transformed Data

Source: R/NormalizationMethods.R
rlrMACycNorm.Rd

No reference, but MA transformation and normalization of samples is done pairwise between two samples with A = average of two samples and M = difference. The process is iterated through all samples pairs. Log2 data should be taken as input (on_raw = FALSE).

Usage

rlrMACycNorm(
  se,
  ain = "log2",
  aout = "RlrMACyc",
  on_raw = FALSE,
  iterations = 3
)

Arguments

se

SummarizedExperiment containing all necessary information of the proteomic dataset

ain

String which assay should be used as input

aout

String which assay should be used to save normalized data

on_raw

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

iterations

Number of cyclic iterations to be performed

Value

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

Examples

data(tuberculosis_TMT_se)
tuberculosis_TMT_se <- rlrMACycNorm(tuberculosis_TMT_se, ain = "log2",
                            aout = "RlrMACyc", on_raw = FALSE, iterations=3)
#> Warning: 'rlm' failed to converge in 20 steps
#> Warning: 'rlm' failed to converge in 20 steps
#> Warning: 'rlm' failed to converge in 20 steps
#> Warning: 'rlm' failed to converge in 20 steps
#> Warning: 'rlm' failed to converge in 20 steps
#> Warning: 'rlm' failed to converge in 20 steps
#> Warning: 'rlm' failed to converge in 20 steps
#> Warning: 'rlm' failed to converge in 20 steps
#> Warning: 'rlm' failed to converge in 20 steps
#> Warning: 'rlm' failed to converge in 20 steps
#> Warning: 'rlm' failed to converge in 20 steps
#> Warning: 'rlm' failed to converge in 20 steps
#> Warning: 'rlm' failed to converge in 20 steps
#> Warning: 'rlm' failed to converge in 20 steps
#> Warning: 'rlm' failed to converge in 20 steps