human.data: Sample ExpressionSet object of human data

In AGDEX: Agreement of Differential Expression Analysis

Description

An ExpressionSet object of human data.

Usage

data(human.data)

Details

human.data is an ExpressionSet object where exprs slot carries the human gene expression data and the pData contains the phenotype data. This sample data human.data is a subset taken from our published study of human brain tumor ependymoma (Johnson et al. 2010). The original full human expression data contains 54,613 probe-sets for 83 human enpendymoma tumors. The gene expression is profiled with Affymetrix U133+2(mRNA) array and the expression data were normalized with MAS 5.0 algorithm.

The expr of human.data is a gene expression matrix with rows of probe-sets and columns representing ependymoma tumors which are classified as belonging to the novel subgroup D or others. Probe-sets in the gene expression matrix are randomly selected from the full human gene profile such that the selected probe-sets belong to the gene-sets in gset.data. pData slot of human.data is a data frame with two columns indicating sample ID and sample group label for each sample(either "human.tumor.typeD" or "other.human.tumors").

Value

expr(human.data)	A matrix with 246 rows and 83 columns with rows representing probe-sets and cloumns of human sample IDs.
pData(human.data)	A data frame with 83 rows and 2 columns. Each row represents one human sample. Column id is the human sample ID and grp is the assigned sample group label.

References

R. Johnson et al.(2010) Cross-species genomics matches driver mutations and cell compartments to model ependymoma. Nature, 466: 632-6.

See Also

ExpressionSet-class

agdex; mouse.data; map.data; gset.data

Examples

data(human.data)
human.express.set <- exprs(human.data)
human.pheno.data <- pData(human.data)

AGDEX documentation built on Nov. 8, 2020, 8:32 p.m.