renal cell cancer raw data

Description

renal cell cancer raw data

Usage

data(qua)
data(spotanno)
data(hybanno)

Format

qua is an 8704x4x175 array. Its first dimension are the spots (probes) on the arrays, its second dimension are four different spot statistics (fg.green, bg.green, fg.red, bg.red), its third dimension are the 175 different arrays.

spotanno is a data frame with 8704 rows, one for each spot. Its columns are: Block, Row, Column, AccNumber, Name, SrcPlt, SrcRow, SrcCol, vendor, ImageID, probe. The column spotanno$probe is of class numeric, with values from 1 to 4224, referring to the rows of cloneanno.

hybanno is a data frame with 175 rows, one for each array. Its columns are: filename, patientid, slideid. The column patientid is of class character, refering to the patients in pData(eset).

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

eset

Examples

data(qua)
qua[1,,1]
data(spotanno)
spotanno[1,]
data(hybanno)
hybanno[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)

R is free software and comes with ABSOLUTELY NO WARRANTY.
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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(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/qua.Rd_%03d_medium.png", width=480, height=480)
> ### Name: qua
> ### Title: renal cell cancer raw data
> ### Aliases: qua spotanno hybanno
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(qua)
> qua[1,,1]
fg.green bg.green   fg.red   bg.red 
 26.5738  22.7030  11.7823   9.8180 
> data(spotanno)
> spotanno[1,]
  Block Row Column AccNumber
1     1   1      1    U40343
                                                                                                  description
1  human cdk inhibitor p19ink4d mrna, complete cds,"cdkn2d","human cdk inhibitor p19ink4d mrna, complete cds"
  SrcPlt SrcRow SrcCol   vendor ImageID probe
1      1      1      4 IMAGp950  145503     1
> data(hybanno)
> hybanno[1,]
             filename patientid slideid
1 00-P09206_E44-1.txt        87   E44-1
> 
> ## see also the vignette
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>