Golub ExpressionSet

Description

This data comes originally from the gene expression data from Golub et al. (1999). The version included in the package is the one used and referenced in Brunet et al. (2004). The samples are from 27 patients with acute lymphoblastic leukemia (ALL) and 11 patients with acute myeloid leukemia (AML).

Format

There are 3 covariates listed.

  • Samples: The original sample labels.
  • ALL.AML: Whether the patient had AML or ALL. It is a factor with levels c('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 a factor with levels c('T-cell', 'B-cell', NA).

Source

Web page for Brunet2004: http://www.broadinstitute.org/publications/broad872

Original data from Golub et al.: http://www-genome.wi.mit.edu/mpr/data_set_ALL_AML.html

Details

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 page related to the paper from Brunet et al. (2004), which describes an application of Nonnegative Matrix Factorization to gene expression clustering. (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.

References

Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP, Coller H, Loh ML, Downing JR, Caligiuri Ma, Bloomfield CD and Lander ES (1999). "Molecular classification of cancer: class discovery and class prediction by gene expression monitoring." _Science (New York, N.Y.)_, *286*(5439), pp. 531-7. ISSN 0036-8075, .

Brunet J, Tamayo P, Golub TR and Mesirov JP (2004). "Metagenes and molecular pattern discovery using matrix factorization." _Proceedings of the National Academy of Sciences of the United States of America_, *101*(12), pp. 4164-9. ISSN 0027-8424, , .

Examples



# requires package Biobase to be installed
if( require(Biobase) ){

    data(esGolub)
    esGolub
    ## Not run: pData(esGolub)

}

## ExpressionSet (storageMode: lockedEnvironment)
## assayData: 5000 features, 38 samples 
##   element names: exprs 
## protocolData: none
## phenoData
##   sampleNames: ALL_19769_B-cell ALL_23953_B-cell ... AML_7 (38
##     total)
##   varLabels: Sample ALL.AML Cell
##   varMetadata: labelDescription
## featureData
##   featureNames: M12759_at U46006_s_at ... D86976_at (5000 total)
##   fvarLabels: Description
##   fvarMetadata: labelDescription
## experimentData: use 'experimentData(object)'
## Annotation: