Normalize each class by its corresponding internal standard(s). Lipid classes are normalized using corresponding internal standard(s) of the same lipid class. If no corresponding internal standard is found the average of all measured internal standards is used instead.
normalize_istd(data, measure = "Area", exclude = "blank", log = TRUE)
Which measure to use as intensity, usually Area,
Area Normalized or Height. Default is
Samples to exclude, can be either:
whether the normalized values should be log2 transformed. Default
A LipidomicsExperiment object with normalized values. Each molecule is normalized against the internal standard from the same class.
datadir <- system.file("extdata", package = "lipidr") filelist <- list.files(datadir, "data.csv", full.names = TRUE) d <- read_skyline(filelist)#>#>#>clinical_file <- system.file("extdata", "clin.csv", package = "lipidr") d <- add_sample_annotation(d, clinical_file) d_summarized <- summarize_transitions(d, method = "average") # Normalize data that have been summarized (single value per molecule). data_norm_istd <- normalize_istd( d_summarized, measure = "Area", exclude = "blank", log = TRUE )#> Warning: Area contains missing/non-finite values. Replacing with mimnum detected value.