human.data: Sample ExpressionSet object of human data

Description Usage Details Value References See Also Examples

Description

An ExpressionSet object of human data.

Usage

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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

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

AGDEX documentation built on May 6, 2019, 2:04 a.m.