ExpressionSet containing ChIP-chip data

Description

Preprocessed ChIP-chexpression data from M. musculus brain and heart cells. H3K4me3 ChIP and input samples were hybridized to a set of four custom NimbleGen microarrays with non-overlapping sets of 390k reporters each. The results were preprocessed per array type and the result fold changes were combinded via rbind afterwards, resulting in this ExpressionSet with 1.5m reporters.

Usage

data(X)

Format

Preprocessed ChIP-chip data as an ExpressionSet with 1495582 features, 2 samples.

Details

This ExpressionSet is created in the vignette, but for purposes of speed and for computers with small RAM, we provide it as a data object here as well.

See Also

ExpressionSet, preprocess

Examples

data("X")
show(X)
pData(X)

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/X.Rd_%03d_medium.png", width=480, height=480)
> ### Name: X
> ### Title: ExpressionSet containing ChIP-chip data
> ### Aliases: X
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data("X")
> show(X)
ExpressionSet (storageMode: lockedEnvironment)
assayData: 1495582 features, 2 samples 
  element names: exprs 
protocolData: none
phenoData
  sampleNames: H3K4me3.brain H3K4me3.heart
  varLabels: SlideNumber FileNameCy3 ... Tissue (8 total)
  varMetadata: varLabel labelDescription
featureData
  featureNames: MM5000P00314500 MM5000P00286227 ... MM5000P14107888
    (1495582 total)
  fvarLabels: GENE_EXPR_OPTION PROBE_ID ... ID (7 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:  
> pData(X)
              SlideNumber    FileNameCy3    FileNameCy5
H3K4me3.brain       48153 48153_532.pair 48153_635.pair
H3K4me3.heart       48170 48170_532.pair 48170_635.pair
                                DESIGN_NAME SAMPLE_SPECIES   Cy3     Cy5 Tissue
H3K4me3.brain 2005-06-17_Ren_MM5Tiling_Set1   Mus_musculus input H3K4me3  brain
H3K4me3.heart 2005-06-17_Ren_MM5Tiling_Set1   Mus_musculus input H3K4me3  heart
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>