omicsTools (version 1.1.7)

pqn_normalize: Perform Probabilistic Quotient Normalization for intensities

Description

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 median spectrum of all samples.

Usage

pqn_normalize(data)

Value

A data frame with the first column as the sample identifiers and the rest of the columns containing the normalized peak intensities.

Arguments

data

A data frame containing the sample data. The first column should contain the sample identifiers, and the rest of the columns contain the peaks to be normalized.

Author

Yaoxiang Li

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

# Load the CSV data
data_file <- system.file("extdata", "example2.csv", package = "omicsTools")
data <- readr::read_csv(data_file)

# Display the first few rows of the original data
print(head(data))

# Apply the pqn_normalize function
normalized_data <- pqn_normalize(data)

# Display the first few rows of the normalized data
print(head(normalized_data))

# \donttest{
# Write the normalized data to a new CSV file
readr::write_csv(normalized_data, paste0(tempdir(), "/normalized_data.csv"))
# }