HGU.newnames: HGU.newnames
In metahdep: Hierarchical Dependence in Meta-Analysis

Description Usage Format Details References Examples

An illustrative example of a data.frame with 3 columns. The first column is named "chip", the second "old.name", and the third "new.name". The rows each hold the name of a chip type, a chip-specific probeset name, and a common name used to match probesets across different chip versions.

1	data(HGU.newnames)

A data.frame with observations on the following 3 variables for a subset of probesets on different chip types.

chip: a character vector specifying the chip type
old.name: a character vector specifying the probeset name on the chip type
new.name: a character vector specifying the common identifier, such as an Entrez Gene ID, for the probeset on the chip type

This is an example of a newnames argument that is required by the metahdep.format function. When paired with a list of ES.obj class objects (see HGU.DifExp.list) this allows the metahdep.format() function to assemble all of the information from all of the studies for a specific gene. The new.name is a 'common' identifier, e.g., an Entrez Gene ID. Different studies may use different chip types, or different versions of chips, where information for a gene with a particular Entrez Gene ID may have a different probeset name on each chip type. This newnames argument is meant to facilitate the matching of gene information across different chip types. See the metahdep package vignette for more details on the construction of this object.

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.