stjude {stjudem} | R Documentation |
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'.
Usage
data(stjude)
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.
Examples
data(stjude)
summary(stjude)
[Package
stjudem version 1.2.0
Index]