stjd: Subset Microarray Data from St.Jude Children Research...

In macat: MicroArray Chromosome Analysis Tool

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)

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)

Note

For the full data package see the Bioconductor data package stjudem. If it is not already installed on your system, try if (!requireNamespace("BiocManager", quietly=TRUE)); install.packages("BiocManager"); BiocManager::install("stjudem")

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

Examples

data(stjd)
summary(stjd)

macat documentation built on Nov. 8, 2020, 5:44 p.m.