Lung Cancer Gene Expression Dataset

Description

This data set contains clinical annotations and the log expression of 150 genes for a set of 444 lung cancer patients. The 150 genes were selected randomly from a larger Affymetrix U133A dataset.

Usage

data(lungData)

Format

A data matrix (lung.dataset) containing the log expression of 150 genes (rows) in 444 lung tumor samples (columns), along with a data frame (lung.clinical) containing clinical annotations of the patients.

Source

Supporting data for the Nature Medicine paper by Shedden et al. was downloaded from the (now defunct) caArray web site. The original data are still available by FTP from ftp://caftpd.nci.nih.gov/pub/caARRAY/experiments/caArray_beer-00153/ and in the Gene Expression Omnibus at http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE68571. The data were log transformed by mapping the expression value x to log2(1+x). A subset of genes and of clinical annotation columns were selected to form this data set.

References

Shedden K, Taylor JM, et al.
Gene expression-based survival prediction in lung adenocarcinoma: a multi-site, blinded validation study.
(Director's Challenge Consortium for the Molecular Classification of Lung Adenocarcinoma).
Nature Medicine 2008; 14(8):822-7.