Barnes Benchmark Illumina Tissues Titration Data

Description

The Barnes data set measured a titration series of two human tissues, blood and placenta. It includes six samples with the titration ratio of blood and placenta as 100:0, 95:5, 75:25, 50:50, 25:75 and 0:100. The samples were hybridized on HumanRef-8 BeadChip (Illumina, Inc) in duplicate. See (Barnes, et al., 2005) for details. The data is saved as a LumiBatch object and should be use together with lumi package.

Because the Barnes data utilized the pre-released version of HumanRef-8 version 1 BeadChip, some probes on the chip do not exist in the public released HumanRef-8 version 1 BeadChip. For annotation consistence, these probes was removed in the lumiBarnes package. For the interested users, the raw data can be downloaded from the paper companion website: http://www.bioinformatics.ubc.ca/pavlidis/lab/platformCompare/.

Usage

data(lumiBarnes)

Format

lumiBarnes is a LumiBatch-class object.

Source

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.

Examples

data(lumiBarnes)
lumiBarnes

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)

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> library(lumiBarnes)
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: lumi
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/lumiBarnes/lumiBarnes.Rd_%03d_medium.png", width=480, height=480)
> ### Name: lumiBarnes
> ### Title: Barnes Benchmark Illumina Tissues Titration Data
> ### Aliases: lumiBarnes
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(lumiBarnes)
> lumiBarnes
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 2007-03-25 02:23:16 2007-03-25 02:25:22
2 2007-03-25 02:25:27 2007-03-25 02:25:29
3 2007-03-25 02:26:00 2007-03-25 02:26:06
4 2007-03-25 02:30:28 2007-03-25 02:30:28
                                             command lumiVersion
1           lumiR("../data/Barnes_gene_profile.txt")       1.1.0
2                             lumiQ(x.lumi = x.lumi)       1.1.0
3 addNuId2lumi(x.lumi = x.lumi, lib = "lumiHumanV1")       1.1.0
4                         Subsetting 21966 features.       1.1.0

Object Information:
LumiBatch (storageMode: lockedEnvironment)
assayData: 21966 features, 16 samples 
  element names: beadNum, detection, exprs, se.exprs 
protocolData: none
phenoData
  sampleNames: A01 A02 ... B08 (16 total)
  varLabels: sampleID label ... replicate (5 total)
  varMetadata: labelDescription
featureData
  featureNames: ZpF0SBA8lTA9BF6Ku4 fl97V6._QueT9ZYg1k ...
    W3oFhJHVApHUkUN4XU (21966 total)
  fvarLabels: TargetID
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation: lumiHumanV1 
Control Data: Available
QC information: Please run summary(x, 'QC') for details!
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>