vdxs: Gene expression, annotations and clinical data from Wang et...

In genefu: Computation of Gene Expression-Based Signatures in Breast Cancer

Description

This dataset contains (part of) the gene expression, annotations and clinical data as published in Wang et al. 2005 and Minn et al 2007.

Usage

data(vdxs)

Format

vdxs is a dataset containing three matrices:

data.vdxs

Matrix containing gene expressions as measured by Affymetrix hgu133a technology (single-channel, oligonucleotides

annot.vdxs

Matrix containing annotations of ffymetrix hgu133a microarray platform

demo.vdxs

Clinical information of the breast cancer patients whose tumors were hybridized

Details

This dataset represent only partially the one published by Wang et al. 2005 and Minn et al 2007. Indeed only part of the patients (150) and gene expressions (966) are contained in data.vdxs.

Source

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2034 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE5327

References

Y. Wang and J. G. Klijn and Y. Zhang and A. M. Sieuwerts and M. P. Look and F. Yang and D. Talantov and M. Timmermans and M. E. Meijer-van Gelder and J. Yu and T. Jatkoe and E. M. Berns and D. Atkins and J. A. Foekens (2005) "Gene-Expression Profiles to Predict Distant Metastasis of Lymph-Node-Negative Primary Breast Cancer", Lancet, 365:671–679

Minn, Andy J. and Gupta, Gaorav P. and Padua, David and Bos, Paula and Nguyen, Don X. and Nuyten, Dimitry and Kreike, Bas and Zhang, Yi and Wang, Yixin and Ishwaran, Hemant and Foekens, John A. and van de Vijver, Marc and Massague, Joan (2007) "Lung metastasis genes couple breast tumor size and metastatic spread", Proceedings of the National Academy of Sciences, 104(16):6740–6745

Examples

data(vdxs)

Example output

Loading required package: survcomp
Loading required package: survival
Loading required package: prodlim
Loading required package: mclust
Package 'mclust' version 5.4.1
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, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, 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, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

genefu documentation built on Jan. 28, 2021, 2:01 a.m.