Log2-scaled data should be used as input (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
- gamma.0
Numeric representing the exponent of the weighted density. When the sample size is small, the fitted population of some proteins could be locally trapped such that the variance of those proteins was very small under a large gamma. To avoid this, a small gamma is recommended. When sample size smaller than 40, then set gamma to 0.5 or 0.1.
Examples
data(tuberculosis_TMT_se)
tuberculosis_TMT_se <- robnormNorm(tuberculosis_TMT_se, ain = "log2",
aout = "RobNorm", on_raw = FALSE, gamma.0 = 0.1)