protti: median_normalisation – R documentation

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median_normalisation

Median normalisation

Description

Performs median normalisation on intensities. The normalised intensity is the original intensity minus the run median plus the global median. This is also the way it is implemented in Spectronaut.

Usage

median_normalisation(data, sample, intensity_log2)

Arguments

`data`	A data frame containing at least sample names and intensity values.
`sample`	The name of the column containing the sample names.
`intensity_log2`	The name of the column containing the log2 transformed intensity values to be normalised.

Value

A dataframe with a column called normalised_intensity_log2 containing the normalised intensity values.

Examples

data <- data.frame(
  r_file_name = c("s1", "s2", "s3", "s1", "s2", "s3"),
  intensity_log2 = c(18, 19, 17, 20, 21, 19)
)

median_normalisation(data,
  sample = r_file_name,
  intensity_log2 = intensity_log2
)

protti

Bottom-Up Proteomics and LiP-MS Quality Control and Data Analysis Tools

v0.1.1

MIT + file LICENSE

Authors

Jan-Philipp Quast [aut, cre], Dina Schuster [aut], ETH Zurich [cph, fnd]

Initial release