Gene expression, annotations and clinical data from the International Genomics Consortium

Description

This dataset contains (part of) the gene expression, annotations and clinical data from the expO dataset collected by the International Genomics Consortium (http://www.intgen.org/expo/).

Usage

data(expos)

Format

expos is a dataset containing three matrices:

data.expos

Matrix containing gene expressions as measured by Affymetrix hgu133plus2 technology (single-channel, oligonucleotides

annot.expos

Matrix containing annotations of ffymetrix hgu133plus2 microarray platform

demo.expos

Clinical information of the breast cancer patients whose tumors were hybridized

Details

This dataset has been generated by the International Genomics Consortium using Affymetrix hgu133plus2 technology. The gene expressions have been normalized using fRMA. Only part of the gene expressions (966) are contained in data.expos.

Source

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2109

References

International Genomics Consortium, http://www.intgen.org/research-services/biobanking-experience/expo/

McCall MN, Bolstad BM, Irizarry RA. (2010) "Frozen robust multiarray analysis (fRMA)", Biostatistics, 11(2):242-253.

Examples

data(expos)

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(genefu)
Loading required package: survcomp
Loading required package: survival
Loading required package: prodlim
Loading required package: mclust
Package 'mclust' version 5.2
Type 'citation("mclust")' for citing this R package in publications.
Loading required package: limma
Loading required package: biomaRt
Loading required package: iC10
Loading required package: pamr
Loading required package: cluster
Loading required package: iC10TrainingData
Loading required package: AIMS
Loading required package: e1071
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 object is masked from 'package:limma':

    plotMA

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")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/genefu/expos.Rd_%03d_medium.png", width=480, height=480)
> ### Name: expos
> ### Title: Gene expression, annotations and clinical data from the
> ###   International Genomics Consortium
> ### Aliases: expos data.expos annot.expos demo.expos
> ### Keywords: data
> 
> ### ** Examples
> 
> data(expos)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>