equalMedianNormalization: normalize to have equal medians in all samples
In DEqMS: a tool to perform statistical analysis of differential protein expression for quantitative proteomics data.
Description
Usage
Arguments
Value
Author(s)
Examples
Description
This function is to normaliza out the differences of protein medians in
different samples
Usage
1
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
1
2
3
4
5
6
7
8
9
10
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)
DEqMS documentation built on Nov. 8, 2020, 7:51 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Usage Arguments Value Author(s) Examples
Description
This function is to normaliza out the differences of protein medians in different samples
Usage
1 |
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
1 2 3 4 5 6 7 8 9 10 | 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)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.