make.dex.set.object: Make a list object for function agdex()
In AGDEX: Agreement of Differential Expression Analysis

Description Usage Arguments Details Value Author(s) See Also Examples

This function generates a list object containing four components for function agdex()

1	make.dex.set.object(Eset.data, comp.var, comp.def, gset.collection)

`Eset.data`	an ExpressionSet object carries the gene expression data (Exprs) and Phenotype data (pData)
`comp.var`	the column name or numeric index for group labels in pData of object Eset.data
`comp.def`	a string definition of comparison, group labels connected by "-"
`gset.collection`	an object belongs to class GeneSetCollection

The ExpressionSet includes two components: exprs: a matrix of expression values pData: a data frame contains the sample IDs and their assigned group labels.

gset.collection contains a GeneSetCollection object defined in the Bioconductor package GSEABase. The gset.collection object must use the same identifiers for probe-sets as that used in the exprs component of Eset.data.

A list object containing the four components described in argument section.

Stan Pounds <stanley.pounds@stjude.org; Cuilan Lani Gao <cuilan.gao@stjude.org>

ExpressionSet class: ExpressionSet.

GeneSetCollection class: GeneSetCollection.

agdex; write.agdex.result; agdex.scatterplot; get.gset.result.details; read.agdex.gset.details; read.agdex.gset.details;

 # load data
 data(human.data)
 data(mouse.data) 
 data(gset.data)                  
 # make dex.set object for human data
 dex.set.human <- make.dex.set.object(human.data,
                                      comp.var=2,
                                      comp.def="human.tumor.typeD-other.human.tumors",
                                      gset.collection=gset.data)
 # make dex.set object for mouse data
 dex.set.mouse <- make.dex.set.object(mouse.data,
                                      comp.var=2,
                                      comp.def="mouse.tumor-mouse.control",
                                      gset.collection=NULL)