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# Description and generation of data
#
# Author: Renaud Gaujoux
###############################################################################
#' Golub ExpressionSet
#'
#' This data comes originally from the gene expression data from \cite{Golub1999}.
#' The version included in the package is the one used and referenced in \cite{Brunet2004}.
#' 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 \code{esGolub} were obtained from the web page related to
#' the paper from \cite{Brunet2004}, which describes an application of
#' Nonnegative Matrix Factorization to gene expression clustering.
#' (see link in section \emph{Source}).
#'
#' They contain the 5,000 most highly varying genes according to their
#' coefficient of variation, and were installed in an object of class
#' \emph{ExpressionSet}.
#'
#' @format There are 3 covariates listed.
#'
#' \itemize{
#'
#' \item Samples: The original sample labels. \item ALL.AML: Whether the
#' patient had AML or ALL. It is a \code{\link{factor}} with levels
#' \code{c('ALL', 'AML')}. \item 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
#' \code{\link{factor}} with levels \code{c('T-cell', 'B-cell', NA)}.
#'
#' }
#'
#' @source
#' Web page for \cite{Brunet2004}:\cr
#' \url{http://www.broadinstitute.org/publications/broad872}
#'
#' Original data from Golub et al.:\cr
#' \url{http://www-genome.wi.mit.edu/mpr/data_set_ALL_AML.html}
#'
#' @name esGolub
#' @docType data
#' @keywords datasets
#' @examples
#'
#' # requires package Biobase to be installed
#' if(requireNamespace("Biobase", quietly=TRUE)){
#'
#' data(esGolub)
#' esGolub
#' \dontrun{pData(esGolub)}
#'
#' }
#'
NULL
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