Create an ExpressionSet containing 2D Gel Volume Data

Description

This function create an an ExpressionSet containing 2D Gel Volume Data and associated metadata. It requires a matrix of 2D Gel Volume data with Gels as columns and Spots as rows as well as a dataframe describing the data.

Usage

ES.prot(data, n1, n2, f)

Arguments

Details

Usually data matrix should be the output of Norm.qt and therefore is log2-transformed. In data the columns (i.e. Gels) must be ordered with replicates from condition 1 before those from condition 2.

Value

The function returns an ExpressionSet. The matrix of spots intensities (i.e. Volume) is stored in the assayData slot of the ExpressionSet and can be retrieved with exprs. In the featureData slot the log2-ratio is computed and can be retrieved with fData.

Author(s)

Sebastien Artigaud sebastien.artigaud@gmx.com

See Also

Norm.qt,Norm.vsn,ExpressionSet

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)
head(exprs(ES.p))

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/ES.prot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ES.prot
> ### Title: Create an ExpressionSet containing 2D Gel Volume Data
> ### Aliases: ES.prot
> ### Keywords: 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)
> head(exprs(ES.p))
    Br_23865 Br_23883 Br_23884 Br_23728 Br_23729 Br_23730 Br_23731 Br_23732
126 21.47163 21.35892 21.94415 20.90299 24.23405 22.89213 22.23592 23.68951
155 18.75859 18.49826 18.54252 19.76490 20.43126 22.29258 22.99830 21.53323
168 19.55404 19.13246 19.92785 19.18569 18.82005 21.00173 23.23065 20.59767
285 18.98169 18.86374 19.47428 19.46090 19.88780 22.07155 21.08111 22.38885
315 17.26368 17.72549 17.83685 18.04834 17.32198 20.71461 21.05901 20.27296
328 18.80816 18.64969 18.38787 17.39618 17.56088 17.05952 17.62784 17.80740
    Br_23733 Br_23875 Br_23876 Br_23877
126 22.10465 20.75666 21.38171 22.78902
155 20.57189 18.75859 18.64378 18.68850
168 21.10489 19.55404 19.33946 20.23641
285 21.48684 19.00240 19.06097 19.19463
315 19.97630 17.89045 16.90358 18.27769
328 19.56859 19.16633 20.20363 20.17508
> 
> 
> 
> 
> dev.off()
null device 
          1 
>