Illumina DASL example microarray data ~~ package title ~~

Description

A subset of GSE17565 (April et al. 2009) containing 32 FFPE samples of Burkitts Lymphoma and Breast Adenocarcinoma, with a dilution series in technical duplicate.

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. The metadata from GEO are also curated for ease of use.

Some analyses of this dataset are done in the ffpe Bioconductor package.

Author(s)

Levi Waldron <lwaldron@hsph.harvard.edu>

References

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

library(lumi)
data(lumibatch.GSE17565)
meta.data <- pData(lumibatch.GSE17565)
expression.data <- exprs(lumibatch.GSE17565)
summary(meta.data)
boxplot(log2(expression.data))

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/ffpeExampleData-package.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ffpeExampleData-package
> ### Title: Illumina DASL example microarray data ~~ package title ~~
> ### Aliases: ffpeExampleData-package ffpeExampleData
> 
> ### ** Examples
> 
> 
> library(lumi)
> data(lumibatch.GSE17565)
> meta.data <- pData(lumibatch.GSE17565)
> expression.data <- exprs(lumibatch.GSE17565)
> summary(meta.data)
    title            inputRNA.ng      cell.type          replicate        
 Length:32          Min.   :  0.01   Length:32          Length:32         
 Class :character   1st Qu.:  0.20   Class :character   Class :character  
 Mode  :character   Median :  3.00   Mode  :character   Mode  :character  
                    Mean   : 20.79                                        
                    3rd Qu.: 20.00                                        
                    Max.   :100.00                                        
    source         
 Length:32         
 Class :character  
 Mode  :character  
                   
                   
                   
> boxplot(log2(expression.data))
Warning message:
In boxplot(log2(expression.data)) : NaNs produced
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>