Perform Probabilistic Quotient Normalization (PQN) for sample intensities. The PQN method determines a dilution factor for each sample by comparing the distribution of quotients between samples and a reference spectrum, followed by sample normalization using this dilution factor. The reference spectrum in this method is the average lipid abundance of all samples (excluding blanks).

normalize_pqn(data, measure = "Area", exclude = "blank", log = TRUE)

Arguments

data

LipidomicsExperiment object.

measure

Which measure to use as intensity, usually Area, Area Normalized or Height. Default is Area.

exclude

Samples to exclude, can be either:
"blank" - automatically detected blank samples and exclude them logical vector with the same length as samples. Default.

log

Whether the normalized values should be log2 transformed. Default is TRUE.

Value

A LipidomicsExperiment object with normalized values

References

Dieterle, F., Ross, A., Schlotterbeck, G., & Senn, H. (2006). Probabilistic quotient normalization as robust method to account for dilution of complex biological mixtures. Application in 1H NMR metabonomics. Analytical chemistry, 78(13), 4281-4290.

Examples

datadir <- system.file("extdata", package = "lipidr")
filelist <- list.files(datadir, "data.csv", full.names = TRUE)