renal cell cancer expression data

Description

renal cell cancer expression data

Usage

data("eset")
data("esetSpot")
data("cloneanno")

Format

eset is an object of type ExpressionSet. Samples (columns of the expression matrix) correspond to renal cell cancer samples from 74 patients with kidney tumors. Probes (rows of the expression matrix) correspond to different cDNA clones.

cloneanno is a data frame with 4224 rows, one for each clone. Its columns are: plate, SrcRow, SrcCol, imageid, AccNumber, spot1, spot2, description, vendor

The arrays that were used to measure these data contained two features for each reporter (clone), and esetSpot is the data before averaging over the two features per reporter. Spots 4225:8448 are the duplicates of spots 1:4224.

Source

Holger Sueltmann, DKFZ. Also available from ArrayExpress, Accession number E-DKFZ-1.

The data import fro Genepix files and Excel tables, and the preprocessing is described in the files preproc.Rnw and preproc.pdf in the scripts subdirectory of the package. Please refer to these for details!

References

Gene expression in kidney cancer is associated with novel tumor subtypes, cytogenetic abnormalities and metastasis formation. Holger Sueltmann, Anja von Heydebreck, Wolfgang Huber, Ruprecht Kuner, Andreas Buness, Markus Vogt, Bastian Gunawan, Martin Vingron, Laszlo Fuezesi, and Annemarie Poustka. Submitted.

See Also

qua

Examples

data(eset)
eset
data(cloneanno)
cloneanno[1,]

## see also the vignette

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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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(kidpack)
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")'.


*** Deprecation warning ***:
The package 'kidpack' is deprecated and will not be supported after Bioconductor release 2.1.


> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/kidpack/eset.Rd_%03d_medium.png", width=480, height=480)
> ### Name: eset
> ### Title: renal cell cancer expression data
> ### Aliases: eset esetSpot cloneanno
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> data(eset)
> eset
ExpressionSet (storageMode: lockedEnvironment)
assayData: 4224 features, 74 samples 
  element names: exprs 
protocolData: none
phenoData
  sampleNames: 1 2 ... 87 (74 total)
  varLabels: lfdnr patientid ... 22q (64 total)
  varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
Annotation:  
> data(cloneanno)
> cloneanno[1,]
  plate SrcRow SrcCol imageid AccNumber spot1 spot2
1     1      1      4  145503    U40343     1  4353
                                                                                                  description
1  human cdk inhibitor p19ink4d mrna, complete cds,"cdkn2d","human cdk inhibitor p19ink4d mrna, complete cds"
    vendor
1 IMAGp950
> 
> ## see also the vignette
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>