GSint2BC {GeneSpring}R Documentation

Convertors for GeneSpring GSint and Bioconductor exprSet objects

Description

These functions convert GeneSpring Experiment (Interpretation) objects into BioConductor expression objects and vice versa.

Usage

expr.set <- GSint2BC(interpretation, what = "nor")
gs.int <- BC2GSint(exprSet)

Arguments

interpretation GeneSpring Expereiment Interpretation object
what For GSload.intBC() only. Indicates what data from the GeneSpring Experiment Interpretation should be used. Valid values for what can be nor and raw, representing Normalized or Raw expression values. The Control values cannot be used.
exprSet GeneSpring Expereiment Interpretation object

Details

The GeneSpring Experiment Interpretation and the BioConductor objects are quite similar, but there are some differences. GeneSpring interpretations can contain information on both normalized and original raw values, and can include, Standard Error, Standard Deviation and number of replicates information, but the BioConductor objects can contain more sample attribute information in the form of the MIAME annotations.

These functions provide convertors for both types of objects.

When converting a GeneSpring object into a BioConductor object, the user has the choice of either using the normalized or raw expression values for the BioConductor exprSet object. Conversely, when a BioConductor objects is converted into a GeneSpring object, the expression values are loaded as normalized values.

The phenoData objects describing the phenotypical data for the samples in a BioConductor object are converted into Experimental Parameter objects in the GeneSpring class object, and vice versa.

The experiment name and any of the other annotations for the BioConductor objects that are stored in the MIAME objects are currently not converted, although future versions of these convertors may provide better mapping.

Value

The return value depends on which fucntion was called. The BC2GSint() function returns an object of class GSint. The GSint2BC() function returns a BioConductor object of class exprSet. See the documentation on GSint and exprSet for more information.

Note

This and any other functions in the GeneSpring package are only useful, when using Agilent Technologies Gene Expression software GeneSpring.

Author(s)

Thon de Boer, Agilent Technologies, Santa Clara, CA, USA thon_deboer@agilent.com

References

For more information on using GeneSpring with R see http://www.chem.agilent.com/scripts/generic.asp?lpage=34733

See Also

GSload.exp, GSload.int, GSsave.exp

Examples

#Use the example data etc. from exprSet
library(Biobase)
data(geneData)
data(geneCov)
covdesc<- list("Covariate 1", "Covariate 2", "Covariate 3")
names(covdesc) <- names(geneCov)
pdata <- new("phenoData", pData=geneCov, varLabels=covdesc)
eset <- new("exprSet", exprs=geneData, phenoData=pdata)

#Convert the objects into GeneSpring objects and back again
gs.int <- BC2GSint(eset)
expr.set <- GSint2BC(gs.int)


[Package GeneSpring version 2.12.0 Index]