leukemia {plsgenomics}

Gene expression data from Golub et al. (1999)

Description

Gene expression data (3051 genes and 38 tumor mRNA samples) from the leukemia microarray study of Golub et al. (1999).

Usage

data(leukemia)

Value

A list with the following elements:

X

a (38 x 3051) matrix giving the expression levels of 3051 genes for 38 leukemia patients. Each row corresponds to a patient, each column to a gene.

Y

a numeric vector of length 38 giving the cancer class of each patient.

gene.names

a matrix containing the names of the 3051 genes for the gene expression matrix X. The three columns correspond to the gene 'index', 'ID', and 'Name', respectively.

Source

The dataset was taken from the R package multtest. The data are described in Golub et al. (1999). The data was originally collected from http://www.broadinstitute.org/cgi-bin/cancer/publications/pub_paper.cgi?paper_id=43 but the URL is not working anymore and we could not find a replacement link in 2024.

References

S. Dudoit, J. Fridlyand and T. P. Speed (2002). Comparison of discrimination methods for the classification of tumors using gene expression data, Journal of the American Statistical Association 97, 77–87.

Golub et al. (1999). Molecular classification of cancer: class discovery and class prediction by gene expression monitoring, Science 286, 531–537.

Examples

# load plsgenomics library
library(plsgenomics)

# load data set
data(leukemia)

# how many samples and how many genes ?
dim(leukemia$X)

# how many samples of class 1 and 2, respectively ?
sum(leukemia$Y==1)
sum(leukemia$Y==2)