Excerpt from GE Codelink array contributions to MAQC

Description

Excerpt from GE Codelink contributions to MAQC

Usage

data(gehSubRaw)
data(gehMAQCsubDef)

Details

gehSubRaw is a codelink::Codelink instance based on reading the raw GEO files: "GSM123122_GEH_1_A1.TXT" "GSM123123_GEH_1_A2.TXT" "GSM123127_GEH_1_B1.TXT" "GSM123128_GEH_1_B2.TXT" "GSM123132_GEH_1_C1.TXT" "GSM123133_GEH_1_C2.TXT" "GSM123137_GEH_1_D1.TXT" "GSM123138_GEH_1_D2.TXT"

gehMAQCsubDef is an ExpressionSet instance based on default background correction and normalization of the codelink package. The original feature names include duplicates; these were made unique by make.names with unique=TRUE.

Author(s)

Vince Carey <stvjc@channing.harvard.edu>

Examples

data(gehMAQCsubDef)
gehMAQCsubDef

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(MAQCsubset)
Loading required package: affy
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

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: lumi
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)

Attaching package: 'lumi'

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

    MAplot, plotDensity

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/MAQCsubset/gehMAQCsubDef.Rd_%03d_medium.png", width=480, height=480)
> ### Name: gehMAQCsubDef
> ### Title: Excerpt from GE Codelink array contributions to MAQC
> ### Aliases: gehMAQCsubDef gehSubRaw
> ### Keywords: models
> 
> ### ** Examples
> 
> data(gehMAQCsubDef)
> gehMAQCsubDef
ExpressionSet (storageMode: lockedEnvironment)
assayData: 54359 features, 8 samples 
  element names: exprs 
protocolData: none
phenoData
  sampleNames: GSM123122_GEH_1_A1.TXT GSM123123_GEH_1_A2.TXT ...
    GSM123138_GEH_1_D2.TXT (8 total)
  varLabels: sampCode repl pctBrain
  varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
  pubMedIds: 16964226 
Annotation: hwgcod 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>