Fast Loess Normalization of limma — loessFNorm • PRONE

Using mean intensities over all the samples as its reference A sample. Log2-scaled data should be used as input (on_raw = FALSE).

Usage

loessFNorm(se, ain = "log2", aout = "LoessF", on_raw = FALSE)

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

Value

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

See also

normalizeCyclicLoess()

Examples

data(tuberculosis_TMT_se)
tuberculosis_TMT_se <- loessFNorm(tuberculosis_TMT_se, ain = "log2",
                                    aout = "LoessCyc", on_raw = FALSE)