stjd {macat} | R Documentation

## Subset Microarry Data from St.Jude Children Research Hospital (USA)

### Description

Example for list-structure used by many functions in MACAT. It's based on the gene expression data published by Yeoh et al. in 2002.[Yeoh et al. Classification, subtype discovery, and prediction of outcome in pediatric acute lymphoblastic leukemia by gene expression profiling. Cancer Cell. March 2002. 1: 133-143. The data has been preprocessed using 'vsn' on probe level and the probes have been summed up using 'median polish'. This is a subset of the data, containg only the 5000 probe sets with the highest across the samples and 10 exemplary samples, 5 from T-lymphocytic Acute Lymphocytic Leukemia (ALL) and 5 from B-lymphocytic ALL.

### Usage

    data(stjd)

### Format

List of class 'MACATData' with 6 components:

geneName:
  Identifiers of genes/probe sets in expression data
geneLocation:
  Location of genes on their chromosome as distance from 5'end in base pairs Negative numbers denote genes on the antisense strand.
chromosome:
  Chromosome of the respective gene. Components 'geneName', 'geneLocation', and 'chromosome' are in the same order.
expr:
  expression matrix with rows = genes and columns = samples/patients
labels:
  (disease) subtype of each sample, has length = number of columns of expression matrix
chip:
  Identifier for Microarray used for the experiments (here for the Affymetrix HG-U95av2 Oligonucleotide GeneChip)

### Source

Yeoh et al. Classification, subtype discovery, and prediction of outcome in pediatric acute lymphoblastic leukemia by gene expression profiling. Cancer Cell. March 2002. 1: 133-143.

### See Also

`buildMACAT`,`stjude` in package 'stjudem' for the complete expression data

### Examples

    data(stjd)
    summary(stjd)

[Package macat version 1.2.0 Index]