stjd: Subset Microarray 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. (2002)
The data has been preprocessed using 'vsn' on probe level and the
probe values have been summed up to probe set values using the
'median polish' procedure.
This is a subset of the data, containing only the data for the 5000
probe sets with the highest variance across the samples and for
10 exemplary samples, 5 from T-lymphocytic Acute Lymphocytic
Leukemia (ALL) and 5 from B-lymphocytic ALL.
Usage
data(stjd)
Arguments
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)
References
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