NMF (version 0.2.2)

esGolub: Golub ExpressionSet from Brunet et al. Paper

Description

The original data is related to Golub et al., and this version is the one used and referenced in Brunet et al. The samples are from 27 patients with acute lymphoblastic leukemia (ALL) and 11 patients with acute myeloid leukemia (AML). The samples were assayed using Affymetrix Hgu6800 chips and the original data on the expression of 7129 genes (Affymetrix probes) are available on the Broad Institute web site (see references below). The data in esGolub were obtained from the web site related to Brunet et al.'s publication on an application of Nonnegative Matrix Factorization (see link in section Source). They contain the 5,000 most highly varying genes according to their coefficient of variation, and were installed in an object of class ExpressionSet-class.

Usage

data(esGolub)

format

There are 3 covariates listed.

• Samples: The original sample labels.
• ALL.AML: Whether the patient had AML or ALL. It is afactorwith levelsc('ALL', 'AML').
• Cell: ALL arises from two different types of lymphocytes (T-cell and B-cell). This specifies which for the ALL patients; There is no such information for the AML samples. It is afactorwith levelsc('T-cell', 'B-cell', NA).

source

http://www.broadinstitute.org/publications/broad872

References

Metagenes and molecular pattern discovery using matrix factorization Brunet, J.~P., Tamayo, P., Golub, T.~R., and Mesirov, J.~P. (2004) Proc Natl Acad Sci U S A 101(12), 4164--4169. Molecular Classification of Cancer: Class Discovery and Class Prediction by Gene Expression Monitoring , Science, 531-537, 1999 , T. R. Golub and D. K. Slonim and P. Tamayo and C. Huard and M. Gaasenbeek and J. P. Mesirov and H. Coller and M.L. Loh and J. R. Downing and M. A. Caligiuri and C. D. Bloomfield and E. S. Lander Original data from Golub et al.: http://www-genome.wi.mit.edu/mpr/data_set_ALL_AML.html

Examples

data(esGolub)
 	esGolub
 	pData(esGolub)