Experimental Data Package: MAQCsubset

Description

selected data from the MAQC project (Nature Biotechnology, Sept. 2006)

Usage

data(afxsubRMAES)
data(afxsubRMA)
data(afxsub)

Format

The format is: An ExpressionSetObject with covariates:

• site: from cel

• samp: rna src/mixture code

• repl: replicate

Note

afxsubRMA is an exprSet (deprecated) and afxsub is an AffyBatch. afxsubRMAES is a proper ExpressionSet instance.

ilmMAQCsubR is the result of applying lumiR to the files in the vicinity of GEO GSM122901 with filename suffixes matching those of the sampleNames in the set.

Examples

  data(afxsubRMAES)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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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/MAQCsubset.Rd_%03d_medium.png", width=480, height=480)
> ### Name: MAQCsubset
> ### Title: Experimental Data Package: MAQCsubset
> ### Aliases: afxsubRMAES afxsubRMA ilmMAQCsubR afxsub MAQCsubset
> ### Keywords: datasets
> 
> ### ** Examples
> 
>   data(afxsubRMAES)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>