\name{khan}
\alias{khan}
\docType{data}
\title{Microarray gene expression dataset from Khan et al., 2001. Subset of 306 genes.}
\description{
 Khan contains gene expression profiles of four types of small round
 blue cell tumours of childhood (SRBCT) published by Khan et
 al. (2001). It also contains further gene annotation retrieved from SOURCE at \url{http://source.stanford.edu/}.
}
\usage{data(khan)}
\format{

 Khan is dataset containing the following:
 \itemize{
    \item{\$train:}{\code{\link{data.frame}} of 306 rows and 64 columns. 
      The training dataset of 64 arrays and 306 gene expression values}
    \item{\$test:}{\code{\link{data.frame}}, of 306 rows and 25 columns. 
      The test dataset of 25 arrays and 306 genes expression values}
    \item{\$gene.labels.imagesID:}{\code{vector} of 306 Image clone identifiers
      corresponding to the rownames of \$train and \$test.}
   \item{\$train.classes:}{\code{\link{factor}} with 4 levels "EWS",
      "BL-NHL", "NB" and "RMS", which correspond to the four groups in 
       the \$train dataset}
    \item{\$test.classes:}{\code{\link{factor}} with 5 levels "EWS",
       "BL-NHL", "NB", "RMS" and "Norm" which correspond to the five 
        groups in the \$test dataset}
   \item{\$annotation:}{\code{\link{data.frame}} of 306 rows and 8 columns. 
       This table contains further gene annotation retrieved from SOURCE 
       \url{http://SOURCE.stanford.edu} in May 2004.  For each of the 306 genes, 
       it contains: \itemize{ 
       \item{\$CloneID}{Image Clone ID}
       \item{\$UGCluster}{The Unigene cluster to which the gene is assigned}
       \item{\$Symbol}{The HUGO gene symbol}
       \item{\$LLID}{The locus ID}
       \item{\$UGRepAcc}{Nucleotide sequence accession number}
       \item{\$LLRepProtAcc}{Protein sequence accession number}
       \item{\$Chromosome}{chromosome location}
       \item{\$Cytoband}{cytoband location} 
         }
       }
   }
}
\details{

 Khan et al., 2001 used cDNA microarrays containing 6567 clones of which
 3789 were known genes and 2778 were ESTs to study the expression of
 genes in of four types of small round blue cell tumours of childhood (SRBCT).  
 These were neuroblastoma (NB), rhabdomyosarcoma (RMS), Burkitt lymphoma, a 
 subset of non-Hodgkin lymphoma (BL), and the Ewing family of tumours
 (EWS). Gene expression profiles from both tumour biopsy and cell line 
 samples were obtained and are contained in this dataset. The dataset downloaded 
 from the website contained the filtered dataset of 2308 gene expression profiles as described
 by Khan et al., 2001.  This dataset is available from the \url{http://bioinf.ucd.ie/people/aedin/R/}.

 In order to reduce the size of the MADE4 package, and produce small example datasets, the top 50 genes from the
 ends of 3 axes following \code{bga} were selected. This produced a reduced datasets of 306 genes. 

}
\source{

 \code{khan} contains a filtered data of 2308 gene expression profiles
  as published and provided by Khan et al. (2001) on the supplementary 
  web site to their publication 
  \url{http://research.nhgri.nih.gov/microarray/Supplement/}.

  
}
\references{
  Culhane AC, et al., 2002 Between-group analysis of microarray
  data. Bioinformatics. 18(12):1600-8.
  
  Khan,J., Wei,J.S., Ringner,M., Saal,L.H., Ladanyi,M., Westermann,F.,
  Berthold,F., Schwab,M., Antonescu,C.R., Peterson,C. et al. (2001) Classification and diagnostic 
  prediction of cancers using gene expression profiling and artificial neural networks. 
  Nat. Med., 7, 673-679.

}
\examples{
data(khan)
summary(khan)
}
\keyword{datasets}