expressionSetList: Example of ExpressionSetList

In XDE: XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression

Description

Object of class ExpressionSetList containing three studies. Each element in the list is an ExpressionSet

Usage

data(expressionSetList)

Details

Parmigiani et al. (2004) performed a cross-study analysis of three lung cancer studies. The studies used in this analysis were merged by UniGene identifiers to obtain a set of 3,171 gene. The R experiment data package lungExpression that was developed to facilitate the reproducibility of this analysis contains the three studies as ExpressionSets. Here, we take a random sample of 500 features from one study (the "stanford" study), and split this study into three artificial studies that each contain 4 squamous carcinomas and 3 adenocarcinomas. The three artificial studies are then used to create an instance of the ExpressionSetList class.

See Garber et al. (2001) for the raw data and description of the stanford study.

Source

The experiment data package lungExpression (www.bioconductor.org)

References

Parmigiani et al. (2004) A cross-study comparison of gene expression studies for the molecular classification of lung cancer, Clin Cancer Res, 10(9): 2922-2927

Garber et al. (2001) Diversity of gene expression in adenocarcinoma of the lung, PNAS, 98:13784-13789

Examples

data(expressionSetList)

XDE documentation built on Nov. 8, 2020, 5:02 p.m.