Barrera expression data

Description

Preprocessed expression data for five M. musculus tissues. Samples were hybridized to Affymetrix's mouse430v2 array platform, preprocessed using the MAS5 method, as implemented in Bioconductor's package affy.

Usage

data(barreraExpressionX)

Format

Preprocessed expression data as an ExpressionSet with 45101 features, 5 samples.

Details

see the supplement for the code chunk that was used to read in the CEL files that are in the expression directory of the package and to preprocess them.

See Also

ExpressionSet, mas5

Examples

data(barreraExpressionX)
show(barreraExpressionX)
## the raw data is here:
dir(system.file("expression", package="ccTutorial"))

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(ccTutorial)
Loading required package: Ringo
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")'.

Loading required package: RColorBrewer
Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

Loading required package: Matrix
Loading required package: grid
Loading required package: lattice
Loading required package: affy

Attaching package: 'affy'

The following object is masked from 'package:Ringo':

    probes

Loading required package: topGO
Loading required package: graph
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:Matrix':

    colMeans, colSums, expand, rowMeans, rowSums

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums


Loading required package: SparseM

Attaching package: 'SparseM'

The following object is masked from 'package:base':

    backsolve


groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.

Attaching package: 'topGO'

The following object is masked from 'package:IRanges':

    members

The following object is masked from 'package:grid':

    depth

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ccTutorial/barreraExpressionX.Rd_%03d_medium.png", width=480, height=480)
> ### Name: barreraExpressionX
> ### Title: Barrera expression data
> ### Aliases: barreraExpressionX
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(barreraExpressionX)
> show(barreraExpressionX)
ExpressionSet (storageMode: lockedEnvironment)
assayData: 45101 features, 5 samples 
  element names: exprs, se.exprs 
protocolData: none
phenoData
  sampleNames: 3024.Ren.Liver.vt.CEL 3026.Ren.Brain.vt.CEL ...
    3062.Ren.RES.vt.CEL (5 total)
  varLabels: sample Tissue
  varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
Annotation: mouse4302 
> ## the raw data is here:
> dir(system.file("expression", package="ccTutorial"))
[1] "3024.Ren.Liver.vt.CEL"         "3026.Ren.Brain.vt.CEL"        
[3] "3060.Ren.Kidney.vt.CEL"        "3061.Ren.Heart.vt.CEL"        
[5] "3062.Ren.RES.vt.CEL"           "barreraExpressionX_mas5.RData"
[7] "process.R"                    
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>