cns {integrativeME}R Documentation

Central Nervous System cancer data, a subset data set from Pomeroy et al. (2002) study

Description

Clinical and a subset of gene expression data from the Pomeroy et al. (2002) study.

Usage

data(breast)

Format

A list containing the following components:

type
vector of lenth 60 indicating the class of the patients (0 = dead, 1 = alive).
cont
data matrix with 60 rows and 500 columns. The gene expression of 500 randomly sampled transcripts (for memory allocation reasons, see details).
indep
data matrix with 60 rows and 5 columns. The measurements of 5 clinical variables. The discrete data are suitable for a MElogreg or MEindep model in the mixture of experts methodology.
loc
data matrix with 60 rows and 4 columns. The measurements of 4 clinical variables. The discrete data are suitable for a MEloc model in the mixture of experts methodology.
loc.ind
indicates the location variable.
gene.name
gives more information on the genes in the cont data set.

Details

Medulloblastomas are embryonal tumors of the central nervous system (CNS). Pomeroy et al. (2002) investigated this malignant brain tumor of childhood as the response of therapy is difficult to predict. The biopsies of 60 patients were obtained before they received any treatment. The expression level of 7,128 genes were available, as well as five clinical variables

For the location model, variables 'Age' and 'Cx' were merged into a single categorical variable (called the location variable).

Source

See website from the refered article. The original data with 7,128 transcripts can be downloaded as an .RData file from http://www.math.univ-toulouse.fr/~lecao/package.html

References

Pomeroy, S.L. and Tamayo, P. and Gaasenbeek, M. and Sturla, L.M. and Angelo, M. and McLaughlin, M.E. and Kim, J.Y.H. and Goumnerova, L.C. and Black, P.M. and Lau, C. and others (2002). Prediction of central nervous system embryonal tumour outcome based on gene expression. Nature, 415, 6870, 436–442.

Hunt, L. and Jorgensen, M. (1999). Mixture model clustering using the MULTIMIX program. Australian & New Zealand Journal of Statistics, 41, 2, 154–171.


[Package integrativeME version 1.1 Index]