mouse.data: Mouse Data

In AGDEX: Agreement of Differential Expression Analysis

Description

mouse.data is an ExpressionSet object where exprs slot carries the mouse gene expression data and pData carries the phenotype data.

Usage

data(mouse.data)

Details

This mouse.data is a subset taken from our published mouse data (Johnson et al. 2010). The original full mouse data was profiled by affymetrix 430 v2(mRNA). It contains 45037 probe-sets for 13 mice brain tumors and 179 normal mice stem cells.

We used the best-match data (available from www.affymetrix.com) as the mapping data of ortholog-matched probe-sets across human gene expression data and mouse gene expression data. expr slot of mouse.data is a matrix of subset of the full mouse gene expression data. Those selected mouse probe-sets are ortholog-matched with human probe-sets in human.data. pData slot of the mouse.data is a data frame with row representing mouse samples and two columns indicating sample IDs and sample group labels for each sample (either "mouse.tumor" or "mouse.control").

Value

expr(mouse.data)	A matrix with 264 rows and 192 columns with rows representing probe-sets and cloumns of mouse sample IDs. Each row name of the matrix is a probe-set Identifier.
pData(mouse.data)	A data frame with 192 rows and 2 columns. Each row represents one mouse sample. Column id is the mouse 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; human.data; map.data; gset.data

Examples

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

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