Ratio-Intensity Plot for 2D Gel Volume data

Description

R-I plots consist in plotting the intensity log2-ratio (R) against mean log10 intensity (I) of spot's volume data from 2D Gel experiments.

Usage

RIplot(data, n1, n2, ...)

Arguments

Details

Dudoit et al (2002) proposed a method for visualization of artifacts in microarray datasets, called the MA-plot, which was transposed for proteomics data as the Ratio-Intensity plot by Meunier et al (2005). R-I plots allow to directly visualize artifacts in the original data set as well as the effects of normalization. The log2-ratio (R) is the log2 of the mean of volume data in condition 2 upon the mean of volume data in condition 1:

R = log2(mean(V_{Cond2})/mean(V_{Cond1}))

The intensity (I) is the log10 of the mean of volume data in condition 2 by the mean of volume data in condition 1

I = log10(mean(V_{Cond2}) x mean(V_{Cond1}))

Value

Display the RI-plot of data, the values on the plot are the number of spots with a Ratio greater then 1 (upper values) or lesser then -1 (lower value). A list is invinsibly returns with components :

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.

• Meunier, B., Bouley, J., Piec, I., Bernard, C., Picard, B., & Hocquette, J.-F. (2005) "Data analysis methods for detection of differential protein expression in two-dimensional gel electrophoresis" Analytical Biochemistry, vol. 340 (2): 226-230.

See Also

Norm.qt,Norm.vsn

Examples

data(pecten)

RIplot(pecten, 6, 6, main="Without Normalization")

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)

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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/RIplot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: RIplot
> ### Title: Ratio-Intensity Plot for 2D Gel Volume data
> ### Aliases: RIplot
> ### Keywords: prot2D
> 
> ### ** Examples
> 
> data(pecten)
> 
> RIplot(pecten, 6, 6, main="Without Normalization")
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>