Example Illumina Expression data in LumiBatch class

Description

Example data as a LumiBatch object which is a subset of Barnes data (Barnes, 2005)

Usage

data(example.lumi)

Format

A 'LumiBatch' object

Details

The data is from (Barnes, 2005). It used Sentrix HumanRef-8 Expression BeadChip. Two samples "100US" and "95US:5P" (each has two technique replicates) were selected. In order to save space, 8000 genes were randomly selected. As a result, the example data includes 8000 genes, each has 4 measurements. The full data set was included in the Bioconductor Experiment data package lumiBarnes.

The entire data set has been built as a lumiBarnes data object and can be downloaded from Bioconductor Experiment Data.

References

Barnes, M., Freudenberg, J., Thompson, S., Aronow, B. and Pavlidis, P. (2005) Ex-perimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platforms, Nucleic Acids Res, 33, 5914-5923.

The detailed data information can be found at: http://www.bioinformatics.ubc.ca/pavlidis/lab/platformCompare/

Examples

## load the data
data(example.lumi)

## summary of the data
example.lumi

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(lumi)
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")'.

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/lumi/example.lumi.Rd_%03d_medium.png", width=480, height=480)
> ### Name: example.lumi
> ### Title: Example Illumina Expression data in LumiBatch class
> ### Aliases: example.lumi
> ### Keywords: datasets
> 
> ### ** Examples
> 
> ## load the data
> data(example.lumi)
> 
> ## summary of the data
> example.lumi
Summary of data information:
Illumina Inc. BeadStudio version 1.4.0.1
		Normalization = none
		Array Content = 11188230_100CP_MAGE-ML.XML
		Error Model = none
		DateTime = 2/3/2005 3:21 PM
		Local Settings = en-US
		

Major Operation History:
            submitted            finished
1 2007-04-22 00:08:36 2007-04-22 00:10:36
2 2007-04-22 00:10:36 2007-04-22 00:10:38
3 2007-04-22 00:13:06 2007-04-22 00:13:10
4 2007-04-22 00:59:20 2007-04-22 00:59:36
                                             command lumiVersion
1           lumiR("../data/Barnes_gene_profile.txt")       1.1.6
2                             lumiQ(x.lumi = x.lumi)       1.1.6
3 addNuId2lumi(x.lumi = x.lumi, lib = "lumiHumanV1")       1.1.6
4            Subsetting 8000 features and 4 samples.       1.1.6

Object Information:
LumiBatch (storageMode: lockedEnvironment)
assayData: 8000 features, 4 samples 
  element names: beadNum, detection, exprs, se.exprs 
protocolData: none
phenoData
  sampleNames: A01 A02 B01 B02
  varLabels: sampleID label
  varMetadata: labelDescription
featureData
  featureNames: oZsQEQXp9ccVIlwoQo 9qedFRd_5Cul.ueZeQ ...
    33KnLHy.RFaieogAF4 (8000 total)
  fvarLabels: TargetID
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation: lumiHumanAll.db 
Control Data: Available
QC information: Please run summary(x, 'QC') for details!
> 
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> 
> dev.off()
null device 
          1 
>