metahdep (version 1.30.0)

HGU.DifExp.list: HGU.DifExp.list: A list of 4 ES.obj objects

Description

An illustrative example of a list summarizing several studies of gene expression. This is used as an example in the meta-analyis of hierarchically dependent gene expression studies.

Usage

data(HGU.DifExp.list)

Format

This object is a list containing 4 ES.obj objects. Each ES.obj object represents the results from a separate gene expression study.

Details

This object has been assembled from existing data as an artificial example; see the vignette for details on its construction. In this example, four studies were conducted, and can be summarized as follows:

Study	Lab	Tissue
Chip	1	1
0	hgu133a	1
1	1	hgu133a
2	1	0
hgu95a	3	2
0	hgu95av2	4
3	1	hgu133b

Notice that study 1 involved two tissue types. The vignette shows how this example supposes that sampling dependence was introduced in study 1 by fitting a gene-specific model with both tissue types simultaneously. Hierarchical dependence is also present in these data because studies 1 and 2 were conducted by the same lab. Each element of HGU.DifExp.list is an ES.obj object in the same format as returned by the getPLM.es() function. Look at the elements of the list (and the vignette) to get an idea of how the data should be laid out.

The intended use for these data is to demonstrate a meta-analysis procedure that accounts for hierarchical dependence between studies. The idea is that results from different studies from the same lab might be dependent. This is an example object that is to be passed as an argument to the metahdep.format() function.

References

Stevens J.R. and Nicholas G. (2009), metahdep: Meta-analysis of hierarchically dependent gene expression studies, Bioinformatics, 25(19):2619-2620.

See also the metahdep package vignette.

Examples

data(HGU.DifExp.list)
head(HGU.DifExp.list[[1]]@ES.mat)
HGU.DifExp.list[[1]]@covariates
##  etc.