choedata {st}R Documentation

A Subset of the Choe et al. (2005) “Golden Spike” Experiment

Description

These data are expression levels for a subset of the genes investigated in the Choe et al. (2005) ``Golden Spike'' Affymetrix case-control experiment.

From the original data the 2,535 probe sets for spike-ins with ratio 1:1 were removed, leaving in total 11,475 genes with 3 replicates per group, and 1,331 known differentially expressed genes.

Usage

data(choedata)

Format

choe2.mat is a matrix of dimension 6 times 11,475. It contains the samples in its rows and the genes in its columns.

choe2.L describes the case control-structure of the experiment, and choe2.degenes indicates the known differentially expressed genes. choe2.symbol.name, choe2.probe.name, and choe2.mapping provide additional information on the investigated genes.

Source

http://genomebiology.com/2005/6/2/r16/abstract/, http://www.ccr.buffalo.edu/halfon/spike/

References

Choe, S. E., M. Boutros, A. M. Michelson, G. M. Church, and M. ~S. Halfon. 2005. Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control data set. Genome Biology 6, R16.

Examples

# load st library
library("st")

# load data set
data(choedata)

# 6 samples, 11,475 genes
dim(choe2.mat)

# two groups (case vs. control
choe2.L

# 1,331 differentially expressed genes
sum(choe2.degenes)

# further information on genes
choe2.symbol.name
choe2.probe.name
choe2.mapping 

[Package st version 1.1.1 Index]