equalMedianNormalization: normalize to have equal medians in all samples

equalMedianNormalizationR Documentation

normalize to have equal medians in all samples

Description

This function is to normaliza out the differences of protein medians in different samples

Usage

equalMedianNormalization(dat)

Arguments

dat

an numeric data frame or matrix containing protein relative abundance in log2 scale

Value

a data frame or matrix with normalized protein relative abundance

Author(s)

Yafeng Zhu

Examples

library(ExperimentHub)
eh = ExperimentHub(localHub=TRUE)
query(eh, "DEqMS")
dat.psm = eh[["EH1663"]]

dat.psm.log = dat.psm
dat.psm.log[,3:12] =  log2(dat.psm[,3:12])
# use the 3 ctrl samples as reference channels to calculate log2 ratio
dat.gene = medianSummary(dat.psm.log,group_col = 2,ref_col =c(3,7,10))
dat.gene.nm = equalMedianNormalization(dat.gene)

yafeng/DEqMS documentation built on Nov. 29, 2024, 1:48 a.m.