Illumina DASL expression data from FFPE tissues.

Description

This lumibatch object contains raw expression data for 32 FFPE samples of Burkitts Lymphoma and Breast Adenocarcinoma, with dilution series and technical duplicates. From the original study by April et al. (2009). Sample metadata includes input RNA concentration, cell type, and replicate #.

Usage

data(lumibatch.GSE17565)

Format

Formal class 'LumiBatch' [package "lumi"]

Details

Downloaded from the GEO URL:

http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GSE17565 .

Raw data were obtained from the supplemental file GSE17565_nonorm_nobkgd.txt.gz, and inserted into a lumibatch object using the lumi:lumiR command.

Source

April C, Klotzle B, Royce T, Wickham-Garcia E et al. Whole-genome gene expression profiling of formalin-fixed, paraffin-embedded tissue samples. PLoS One 2009 Dec 3;4(12):e8162. PMID: 19997620

Data from accession ID GSE17565 of the Gene Expression Omnibus

Examples

data(lumibatch.GSE17565)
meta.data <- pData(lumibatch.GSE17565)
expression.data <- exprs(lumibatch.GSE17565)

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(ffpeExampleData)
Loading required package: 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/ffpeExampleData/lumibatch.GSE17565.Rd_%03d_medium.png", width=480, height=480)
> ### Name: lumibatch.GSE17565
> ### Title: Illumina DASL expression data from FFPE tissues.
> ### Aliases: lumibatch.GSE17565
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> data(lumibatch.GSE17565)
> meta.data <- pData(lumibatch.GSE17565)
> expression.data <- exprs(lumibatch.GSE17565)
> 
> 
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>