Log2-scaled data should be used as input (on_raw = FALSE).
Examples
data(tuberculosis_TMT_se)
tuberculosis_TMT_se <- eigenMSNorm(tuberculosis_TMT_se, ain = "log2",
aout = "EigenMS", on_raw = FALSE)
#> [1] "Data dimentions: "
#> [1] 301 20
#> [1] "Treatmenet groups:"
#> [1] ref HC PTB HC PTB HC PTB TBL TBL TBL ref Rx HC Rx HC Rx HC PTB PTB
#> [20] PTB
#> Levels: ref HC PTB TBL Rx
#> [1] "Selecting complete peptides"
#> [1] "Got 2+ treatment grps"
#> [1] "Computing SVD, estimating Eigentrends..."
#> [1] "Number of treatments: 5"
#> [1] "Number of complete peptides (and samples) used in SVD"
#> [1] 5 20
#> [1] "Number of treatment groups (in svd.id): 5"
#> [1] "Starting Bootstrap....."
#> [1] "Iteration 50"
#> [1] "Iteration 100"
#> [1] "Iteration 150"
#> [1] "Iteration 200"
#> [1] "Iteration 250"
#> [1] "Iteration 300"
#> [1] "Iteration 350"
#> [1] "Iteration 400"
#> [1] "Iteration 450"
#> [1] "Iteration 500"
#> [1] "Number of significant eigenpeptides/trends 1"
#> [1] "Preparing to plot..."
#> [1] "Unique number of treatment combinations: 5"
#> [1] "Normalizing..."
#> [1] "Processing peptide 100"
#> [1] "Done with normalization!!!"