exprso (version 0.1.7)

GSE2eSet: Convert GSE to eSet

Description

A convenience function that builds an eSet object from a GSE data source.

Usage

GSE2eSet(gse, colBy, colID)

Arguments

gse

A GSE data object retrieved using GEOquery.

colBy

A character string. The GSE column name that contains the feature value. If missing, function will prompt user for a column name after previewing options.

colID

A character string. The GSE column name that contains the feature identity. If missing, function will prompt user for a column name after previewing options.

Value

An ExpressionSet object.

Details

The NCBI GEO hosts files in GSE or GDS format, the latter of which exists as a curated version the former. These GDS data files easily convert to an ExpressionSet (abbreviated eSet) object using the GDS2eSet function available from the GEOquery package. However, not all GSE data files have a corresponding GDS data file available. To convert GSE data files into eSet objects, exprso provides this convenience function.

However, the user should note that GSE data files do not always get stored in an easy to parse format. Although this function has worked succesfully with some GSE data files, we cannot make any guarantee that it will work for all GSE data files.

To acquire GSE data files, use the function getGEO from the GEOquery package (e.g., getGEO("GSExxxxx", GSEMatrix = FALSE)). For more information, see the GEOquery package.

See Also

ExprsArray-class, arrayExprs