normalizeTMT: Normalize protein/peptide data using CONSTANd normalization

In bartongroup/Proteus: Downstream analysis of the MaxQuant output

Normalize protein/peptide data using CONSTANd normalization

Description

Normalize protein/peptide data using CONSTANd normalization

Usage

normalizeTMT(pdat, max.iter = 50, eps = 1e-05)

Arguments

pdat	A proteusData object with peptide or protein intensities.
max.iter	Maximum number of iterations for the RAS procedure.
eps	Convergence limit for the RAS procedure.

Details

normalizeTMT implements CONSTANd algorithm from Maes et al. (2016) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4974351/pdf/zjw2779.pdf. It normalizes TMT table, for each experiment separately. After normalization each row shows the percentage of total row intensity and each column is normalized to their mean value. Hence, both row and column means are equal 1/n, where n is the number of columns (reporters).

Value

A proteusData with normalized data.

Examples

library(proteusTMT)
data(proteusTMT)
prodat.norm <- normalizeTMT(prodat)

bartongroup/Proteus documentation built on April 22, 2023, 5:33 a.m.