choedata {st}

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.

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