R: Normalize 2D Gel Volume data using Quantiles Normalization
Norm.qt
R Documentation
Normalize 2D Gel Volume data using Quantiles Normalization
Description
This function allows to normalize 2D Gel Volume data using the Quantiles Normalization.
Usage
Norm.qt(data, n1, n2, plot = T)
Arguments
data
a dataframe of raw 2D Gel Volume data. data should be raw intensities displayed with gel as columns with the name of columns corresponding to the names of the gels and spots as rows with the names of the rows corresponding to the name of the spots. The replicates for each condition should be ordered in following columns.
n1
an integer. Number of replicates in condition 1.
n2
an integer. Number of replicates in condition 2.
plot
logical. if TRUE (default) displaying two RIplot, one with the raw data, another with normalized data.
Details
2D Gel Volume data must be normalized in order to remove systemic variation prior to data analysis. The principle of the "quantiles normalization" is to set each quantile of each column (i.e. the spots volume data of each gels) to the mean of that quantile across gels. The intention is to make all the normalized columns have the same empirical distribution.This function is based on normalizeQuantiles from limma package.
Value
The function returns a matrix of log2 transformed quantiles normalized data
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(prot2D)
Loading required package: fdrtool
Loading required package: st
Loading required package: sda
Loading required package: entropy
Loading required package: corpcor
Loading required package: samr
Loading required package: impute
Loading required package: matrixStats
matrixStats v0.50.2 (2016-04-24) successfully loaded. See ?matrixStats for help.
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Loading required package: limma
Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
plotMA
Loading required package: Mulcom
Loading required package: fields
Loading required package: spam
Loading required package: grid
Spam version 1.3-0 (2015-10-24) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.
Attaching package: 'spam'
The following objects are masked from 'package:base':
backsolve, forwardsolve
Loading required package: maps
# maps v3.1: updated 'world': all lakes moved to separate new #
# 'lakes' database. Type '?world' or 'news(package="maps")'. #
Loading required package: MASS
Loading required package: qvalue
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/prot2D/Norm.qt.Rd_%03d_medium.png", width=480, height=480)
> ### Name: Norm.qt
> ### Title: Normalize 2D Gel Volume data using Quantiles Normalization
> ### Aliases: Norm.qt
> ### Keywords: prot2D
>
> ### ** Examples
>
> data(pecten)
>
> pecten.norm <- Norm.qt(pecten, n1=6, n2=6, plot=TRUE)
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> dev.off()
null device
1
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