Normalize 2D Gel Volume data using VSN

Description

This function allows to normalize 2D Gel Volume data using the "Variance Stabilizing Normalization".

Usage

Norm.vsn(data, n1, n2, plot = T)

Arguments

Details

The "Variance Stabilizing Normalization" relies on a transformation h, of the parametric form h(x)= arsinh(a+bx) (for details see, Huber et al., 2002). The parameters of h together with those of the calibration between experiments are estimated with a robust variant of maximum-likelihood estimation.This function is based on normalizeVSN from limma package.

Value

The function returns a matrix of vsn normalized data

Author(s)

Sebastien Artigaud sebastien.artigaud@gmx.com

References

• Artigaud, S., Gauthier, O. & Pichereau, V. (2013) "Identifying differentially expressed proteins in two-dimensional electrophoresis experiments: inputs from transcriptomics statistical tools." Bioinformatics, vol.29 (21): 2729-2734.

• Huber, W., Heydebreck, von, A., Sultmann, H., Poustka, A., & Vingron, M. (2002) "Variance stabilization applied to microarray data calibration and to the quantification of differential expression" Bioinformatics, vol. 18 (Suppl 1): S96-S104.

See Also

normalizeVSN,RIplot,ES.prot

Examples

data(pecten)

pecten.norm <- Norm.vsn(pecten, n1=6, n2=6, plot=TRUE)

Results

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.vsn.Rd_%03d_medium.png", width=480, height=480)
> ### Name: Norm.vsn
> ### Title: Normalize 2D Gel Volume data using VSN
> ### Aliases: Norm.vsn
> ### Keywords: prot2D
> 
> ### ** Examples
> 
> data(pecten)
> 
> pecten.norm <- Norm.vsn(pecten, n1=6, n2=6, plot=TRUE)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>