Statistics Tools for data issued from a 2D Gel Electrophoresis

Description

The purpose of this package is to analyze (i.e. Normalize and select significant spots) data issued from 2D GEl experiments

Details

This package provides a simple interface for analysing data from 2D gel experiments. Functions for performing normalization as well as selecting significant spots are provided. All the functions for selecting significant spots are adapted from functions for microarray analysis provided by Bioconductor and CRAN, and all credits go to the authors of these functions. For analyzing 2D gel experiments data, users are advised to follow theses steps :

1. Normalize data using Norm.qt

2. Coerce data into an ExpressionSet using ES.prot

3. Use normalized data to find differentially expressed proteins with FDR-controled functions: modT.Prot was find to be the more efficient for 2-DE (see Artigaud et al , 2013) but other functions are provided (ttest.Prot,samT.Prot,efronT.Prot, ,shrinkT.Prot)

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.

• Dudoit, S., Yang, Y.H., Callow, M.J., & Speed, T.P. (2002) "Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments" Statistica Sinica, vol. 12: 111-139.

• Strimmer, K. (2008) "A unified approach to false discovery rate estimation." BMC Bioinformatics, vol. 9: 303.

See Also

ExpressionSet, fdrtool

Examples

data(pecten)
data(pecten.fac)

pecten.norm <- Norm.qt(pecten, n1=6, n2=6, plot=TRUE) #Quantiles normalization of the data
ES.p <- ES.prot(pecten.norm, n1=6, n2=6, f=pecten.fac)
x <- modT.Prot(ES.p, fdr.thr=0.1, plot=TRUE)
featureNames(x) # Names of the spots selected for a moderated t-test with a fdr of 0.1
fData(x) # Displaying fold change (as log2(ratio)) for selected spots
exprs(x) # Normalized volume data for all the selected spots
## Not run: heatplot(x) #Great heatmap of the selected spots (requires made4 Bioconductor package )

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/prot2D-package.Rd_%03d_medium.png", width=480, height=480)
> ### Name: prot2D-package
> ### Title: Statistics Tools for data issued from a 2D Gel Electrophoresis
> ### Aliases: prot2D-package prot2D
> ### Keywords: package biology proteomic 2DGel prot2D
> 
> ### ** Examples
> 
> data(pecten)
> data(pecten.fac)
> 
> pecten.norm <- Norm.qt(pecten, n1=6, n2=6, plot=TRUE) #Quantiles normalization of the data
> ES.p <- ES.prot(pecten.norm, n1=6, n2=6, f=pecten.fac)
> x <- modT.Prot(ES.p, fdr.thr=0.1, plot=TRUE)
Number of up-regulated spots in Condition 2
[1] 0
Number of down-regulated spots in Condition 2
[1] 1
Warning message:
In fitFDistRobustly(var, df1 = df, covariate = covariate, winsor.tail.p = winsor.tail.p) :
  small x values have been offset away from zero
> featureNames(x) # Names of the spots selected for a moderated t-test with a fdr of 0.1
[1] "2607"
> fData(x) # Displaying fold change (as log2(ratio)) for selected spots
         ratio
2607 -1.912657
> exprs(x) # Normalized volume data for all the selected spots
     Br_23865 Br_23883 Br_23884 Br_23728 Br_23729 Br_23730 Br_23731 Br_23732
2607 23.21036   23.454 20.22889 22.34141 23.07774  23.0274 22.63096 20.07119
     Br_23733 Br_23875 Br_23876 Br_23877
2607 21.07323 20.52232 20.02905 19.53711
> ## Not run: heatplot(x) #Great heatmap of the selected spots (requires made4 Bioconductor package )
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>