KODAMA (version 0.0.1)

lymphoma: Lymphoma Gene Expression Dataset

Description

This dataset consists of gene expression profiles of the three most prevalent adult lymphoid malignancies: diffuse large B-cell lymphoma (DLBCL), follicular lymphoma (FL), and B-cell chronic lymphocytic leukemia (B-CLL). The dataset consists of 4,682 genes in 62 mRNA samples: 42 samples of DLBCL, 9 samples of FL, and 11 samples. of B-CLL. Missing value are imputed and data are standardized as described in Dudoit, et al. (2002).

Usage

data(lymphoma)

Value

A list with the following elements:

data

Gene expression data. A matrix with 62 rows and 4,682 columns.

class

Class index. A vector with 62 elements.

References

Alizadeh AA, Eisen MB, Davis RE, et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 2000;403(6769):503-511.

Dudoit S, Fridlyand J, Speed TP. Comparison of discrimination methods for the classification of tumors using gene expression data. J Am Stat Assoc 2002;97(417):77-87.

Examples

data(lymphoma)
class=1+as.numeric(as.factor(unlist(lymphoma$class)))
cc=cmdscale(dist(lymphoma$data))
plot(cc,pch=21,bg=class,xlab="First Component",ylab="Second Component");

# WARNING: The next example is high computational extensive
#
# kk=KODAMA(lymphoma$data,FUN=PLS.SVM.CV)
# cc=cmdscale(kk$dissimilarity)
# plot(cc,pch=21,bg=class,xlab="First Component",ylab="Second Component");